Variant report

Variant	esv3360665
Chromosome Location	chr19:42398332-42399347
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	BCL3	chr19:42397984-42398446	A549	lung:	n/a	n/a
2	CBX3	chr19:42397988-42398335	K562	blood:	n/a	n/a
3	CREB1	chr19:42398063-42398418	A549	lung:	n/a	n/a
4	CTCF	chr19:42399302-42399303	H1-hESC	embryonic stem cell:	n/a	n/a
5	CTCF	chr19:42399309-42399381	H1-hESC	embryonic stem cell:	n/a	chr19:42399354-42399363
6	CTCF	chr19:42398077-42398333	MCF-7	breast:	n/a	chr19:42398170-42398188
7	CTCF	chr19:42398200-42398350	AG09309	skin:	n/a	n/a
8	CTCF	chr19:42398240-42398390	HFF	foreskin:	n/a	n/a
9	CTCF	chr19:42398071-42398356	HepG2	liver:	n/a	chr19:42398170-42398188
10	CTCF	chr19:42397842-42398859	A549	lung:	n/a	chr19:42398170-42398188
11	CTCF	chr19:42398220-42398370	A549	lung:	n/a	n/a
12	CTCF	chr19:42398089-42398336	IMR90	lung:	n/a	chr19:42398170-42398188
13	CTCF	chr19:42398066-42398341	GM12878	blood:	n/a	chr19:42398170-42398188
14	CTCF	chr19:42397977-42398372	K562	blood:	n/a	chr19:42398170-42398188
15	CTCF	chr19:42398076-42398346	MCF-7	breast:	n/a	chr19:42398170-42398188
16	ELF1	chr19:42397983-42398364	A549	lung:	n/a	n/a
17	ELF1	chr19:42397945-42398399	GM12878	blood:	n/a	n/a
18	ELF1	chr19:42398017-42398346	HepG2	liver:	n/a	n/a
19	ETS1	chr19:42397978-42398400	A549	lung:	n/a	chr19:42398130-42398141 chr19:42398129-42398143 chr19:42398129-42398138
20	FOXA2	chr19:42398087-42398386	A549	lung:	n/a	n/a
21	GABPA	chr19:42398013-42398429	A549	lung:	n/a	n/a
22	GABPA	chr19:42398012-42398549	A549	lung:	n/a	n/a
23	GABPA	chr19:42398005-42398344	K562	blood:	n/a	n/a
24	GABPA	chr19:42398012-42398374	K562	blood:	n/a	n/a
25	MAZ	chr19:42398016-42398402	IMR90	lung:	n/a	n/a
26	MYBL2	chr19:42397906-42398462	HepG2	liver:	n/a	n/a
27	PBX3	chr19:42398600-42398744	GM12878	blood:	n/a	n/a
28	POLR2A	chr19:42398068-42398567	HepG2	liver:	n/a	n/a
29	POLR2A	chr19:42398145-42398358	GM12878	blood:	n/a	n/a
30	POLR2A	chr19:42398507-42398528	K562	blood:	n/a	n/a
31	POLR2A	chr19:42399251-42399549	K562	blood:	n/a	n/a
32	POLR2A	chr19:42398084-42398435	GM12892	blood:	n/a	n/a
33	POLR2A	chr19:42398691-42398772	HepG2	liver:	n/a	n/a
34	POLR2A	chr19:42398260-42398414	K562	blood:	n/a	n/a
35	POLR2A	chr19:42398119-42398798	HL-60	blood:	n/a	n/a
36	RAD21	chr19:42397995-42398390	HepG2	liver:	n/a	n/a
37	RAD21	chr19:42398059-42398355	HepG2	liver:	n/a	n/a
38	RAD21	chr19:42398017-42398369	H1-hESC	embryonic stem cell:	n/a	n/a
39	REST	chr19:42398088-42398360	H1-hESC	embryonic stem cell:	n/a	n/a
40	SIN3AK20	chr19:42398003-42398373	A549	lung:	n/a	n/a
41	SPI1	chr19:42398552-42398783	GM12891	blood:	n/a	chr19:42398637-42398650
42	SPI1	chr19:42398548-42398860	GM12878	blood:	n/a	chr19:42398637-42398650
43	SPI1	chr19:42398426-42399014	GM12878	blood:	n/a	chr19:42398637-42398650
44	TCF12	chr19:42398553-42398797	GM12878	blood:	n/a	chr19:42398658-42398668
45	TCF12	chr19:42398566-42398784	GM12878	blood:	n/a	chr19:42398658-42398668
46	TCF12	chr19:42397898-42398519	A549	lung:	n/a	n/a
47	ZNF263	chr19:42398129-42398352	HEK293-T-REx	kidney:	n/a	n/a
48	ZNF263	chr19:42398919-42399402	HEK293-T-REx	kidney:	n/a	chr19:42399227-42399248

No.	Distal block	Cell Line	Cell type
1	chr19:42398480..42400174-chr19:42432062..42434996,2	K562	blood:
2	chr19:42397636..42399907-chr19:42401318..42404591,3	K562	blood:
3	chr19:42398848..42401100-chr19:42409902..42411983,2	MCF-7	breast:
4	chr19:42399244..42402499-chr19:42406088..42408738,6	MCF-7	breast:

Variant related genes	Relation type
ARHGEF1	TF binding region
ENSG00000076928	chromatin interactions

Extended variants
information (count: 69 )
Associated
traits (count: 61 )

Variant overlapped rSNPs/rCNVs (count:69 , 50 per page) page: 1 2

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs368940793	chr19:42398354-42398355	Weak transcription Strong transcription Genic enhancers Enhancers	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
2	rs539561941	chr19:42398355-42398356	Weak transcription Strong transcription Genic enhancers Enhancers	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
3	rs188938411	chr19:42398395-42398396	Weak transcription Strong transcription Genic enhancers Enhancers	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
4	rs370278424	chr19:42398412-42398413	Weak transcription Strong transcription Genic enhancers Enhancers	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
5	rs552631968	chr19:42398425-42398426	Weak transcription Strong transcription Genic enhancers Enhancers	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
6	rs374677524	chr19:42398427-42398428	Weak transcription Strong transcription Genic enhancers Enhancers	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
7	rs149993474	chr19:42398432-42398433	Weak transcription Strong transcription Genic enhancers Enhancers	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
8	rs12104228	chr19:42398450-42398451	Weak transcription Strong transcription Genic enhancers Enhancers	TF binding region Chromatin interactive region	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
9	rs546989400	chr19:42398458-42398459	Weak transcription Strong transcription Genic enhancers Enhancers	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
10	rs145191723	chr19:42398476-42398477	Weak transcription Strong transcription Genic enhancers Enhancers	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
11	rs371929877	chr19:42398479-42398480	Weak transcription Strong transcription Genic enhancers Enhancers	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
12	rs557324472	chr19:42398490-42398491	Weak transcription Strong transcription Genic enhancers Enhancers	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
13	rs374846976	chr19:42398521-42398522	Weak transcription Strong transcription Genic enhancers Enhancers	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
14	rs142729688	chr19:42398536-42398537	Weak transcription Strong transcription Genic enhancers Enhancers	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
15	rs370981860	chr19:42398543-42398544	Weak transcription Strong transcription Genic enhancers Enhancers	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
16	rs202000253	chr19:42398547-42398548	Weak transcription Strong transcription Genic enhancers Enhancers	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
17	rs374051481	chr19:42398577-42398578	Weak transcription Strong transcription Genic enhancers Enhancers	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
18	rs147557273	chr19:42398590-42398591	Weak transcription Strong transcription Genic enhancers Enhancers	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
19	rs141980059	chr19:42398592-42398593	Weak transcription Strong transcription Genic enhancers Enhancers	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
20	rs372584820	chr19:42398662-42398663	Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
21	rs375847373	chr19:42398681-42398682	Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
22	rs369697433	chr19:42398687-42398688	Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
23	rs149118514	chr19:42398692-42398693	Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
24	rs145833533	chr19:42398717-42398718	Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
25	rs376890229	chr19:42398740-42398741	Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
26	rs539960808	chr19:42398767-42398768	Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
27	rs144864376	chr19:42398769-42398770	Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
28	rs113775444	chr19:42398816-42398817	Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
29	rs113166807	chr19:42398820-42398821	Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
30	rs138696824	chr19:42398822-42398823	Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
31	rs534778260	chr19:42398823-42398824	Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
32	rs140317900	chr19:42398824-42398825	Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
33	rs563679072	chr19:42398827-42398828	Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
34	rs76734442	chr19:42398841-42398842	Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
35	rs564725176	chr19:42398855-42398856	Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
36	rs112702674	chr19:42398858-42398859	Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
37	rs111253296	chr19:42398872-42398873	Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
38	rs544440281	chr19:42398888-42398889	Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
39	rs528545949	chr19:42398895-42398896	Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
40	rs547152599	chr19:42398904-42398905	Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
41	rs568445889	chr19:42398927-42398928	Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
42	rs529356471	chr19:42398935-42398936	Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
43	rs117568517	chr19:42398949-42398950	Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
44	rs569013797	chr19:42398950-42398951	Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
45	rs539720802	chr19:42398954-42398955	Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
46	rs557637587	chr19:42398959-42398960	Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
47	rs112790985	chr19:42398960-42398961	Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
48	rs141681527	chr19:42398963-42398964	Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
49	rs533626803	chr19:42398974-42398975	Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
50	rs7257557	chr19:42398975-42398976	Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:61)

Disease	PMID	Source
Myelodysplastic syndrome	17634407	CNVD
Acute lymphoblastic leukemia	22237106	CNVD
Chordoma	21602918	CNVD
Ewing''s sarcoma	21437220	CNVD
Glioblastoma multiforme	21080181	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Cancer	21637783	CNVD
Retinoblastoma	21504564	CNVD
Medulloblastoma	21979893	CNVD
Ovarian cancer	21720365	CNVD
Cancer	20164919	CNVD
Thoracic aortic aneurysm	21092924	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Prostate cancer	18632612	CNVD
Autism	22495311	CNVD
Adenoid cystic carcinoma	18698036	CNVD
Ductal carcinoma	22052326	CNVD
Congenital nephrotic syndrome	18421352	CNVD
Astrocytoma	17934521	CNVD
Leukemia	17361228	CNVD
Adenoid cystic carcinoma	17372589	CNVD
Breast cancer	21858162	CNVD
Breast cancer	17603634	CNVD
Glioma	21971842	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Endometrial cancer	22040021	CNVD
Astrocytoma	17387387	CNVD
Breast cancer	21264507	CNVD
Oligodendroglial tumors	17285580	CNVD
renal disease	20603712	CNVD
Salivary gland adenoid cystic carcinoma	17545515	CNVD
Ovarian cancer	22174824	CNVD
Breast cancer	16608533	CNVD
Neuroblastoma	18923191	CNVD
Breast cancer	21364760	CNVD
Invasive pancreatic ductal carcinoma	18765526	CNVD
Rhabdomyosarcoma	16790082	CNVD
Chordoma	18071362	CNVD
Urothelial carcinoma	21177765	CNVD
small cell lung cancer	20016488	CNVD
Wilms tumour	21544195	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Ovarian neoplasms	16753589	CNVD
Malignant fibrous histiocytomas	21085701	CNVD
Metanephric adenoma	20802469	CNVD
Acute myeloid leukemia	16864856	CNVD
Bladder cancer	21909424	CNVD
Medulloblastoma	16783165	CNVD
Gastric cancer	18160780	CNVD
Hepatocellular carcinoma	16750200	CNVD
Basal cell lymphoma	19029149	CNVD
Breast cancer	20409316	CNVD
Diffuse large b-cell lymphoma	19029149	CNVD
Multiple myeloma	16616336	CNVD
Renal cell carcinoma	18765545	CNVD
Acute myeloid leukemia	20729466	CNVD
Lung cancer	18438408	CNVD
Genital abnormality	22378287	CNVD
Hypospadia	22378287	CNVD
Ovarian clear cell carcinoma	19293255	CNVD
Astrocytoma	22246337	CNVD

Chromatin state (count:144 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:42389200-42407200	Weak transcription	Fetal Kidney	kidney
2	chr19:42389200-42429200	Weak transcription	Right Atrium	heart
3	chr19:42389400-42402000	Weak transcription	Psoas Muscle	Psoas
4	chr19:42389400-42406000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr19:42389400-42411400	Weak transcription	Fetal Brain Male	brain
6	chr19:42389800-42409000	Strong transcription	Fetal Stomach	stomach
7	chr19:42390800-42411200	Weak transcription	Hela-S3	cervix
8	chr19:42391400-42407400	Weak transcription	K562	blood
9	chr19:42391600-42399600	Weak transcription	HUVEC	blood vessel
10	chr19:42391600-42404600	Weak transcription	HSMM	muscle
11	chr19:42392000-42399600	Strong transcription	Lung	lung
12	chr19:42392000-42404000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr19:42392000-42412600	Strong transcription	Primary monocytes fromperipheralblood	blood
14	chr19:42392000-42412600	Strong transcription	Cortex derived primary cultured neurospheres	brain
15	chr19:42392000-42412600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr19:42392200-42400800	Strong transcription	Skeletal Muscle Male	skeletal muscle
17	chr19:42392200-42401400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
18	chr19:42392200-42407600	Strong transcription	Sigmoid Colon	Sigmoid Colon
19	chr19:42392200-42408400	Strong transcription	Liver	Liver
20	chr19:42392200-42412400	Strong transcription	Fetal Muscle Leg	muscle
21	chr19:42392200-42412800	Strong transcription	Monocytes-CD14+_RO01746	blood
22	chr19:42392400-42399200	Weak transcription	Fetal Lung	lung
23	chr19:42392400-42399600	Weak transcription	Small Intestine	intestine
24	chr19:42392400-42399800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
25	chr19:42392400-42400400	Strong transcription	Stomach Smooth Muscle	stomach
26	chr19:42392400-42401800	Weak transcription	HUES64 Cell Line	embryonic stem cell
27	chr19:42392400-42407600	Strong transcription	Fetal Intestine Small	intestine
28	chr19:42392400-42410200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
29	chr19:42392400-42412400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr19:42392400-42413200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr19:42392600-42399800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
32	chr19:42392600-42400600	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
33	chr19:42392600-42402200	Strong transcription	Adipose Nuclei	Adipose
34	chr19:42392600-42406200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr19:42392600-42407400	Strong transcription	Colonic Mucosa	Colon
36	chr19:42392600-42411800	Strong transcription	Placenta	Placenta
37	chr19:42392600-42413600	Strong transcription	Primary neutrophils fromperipheralblood	blood
38	chr19:42392800-42398800	Genic enhancers	Fetal Thymus	thymus
39	chr19:42392800-42400400	Strong transcription	NHEK	skin
40	chr19:42392800-42400800	Strong transcription	Brain Inferior Temporal Lobe	brain
41	chr19:42392800-42401000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr19:42392800-42402400	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
43	chr19:42392800-42407800	Strong transcription	Fetal Intestine Large	intestine
44	chr19:42393000-42403600	Genic enhancers	Primary T helper cells fromperipheralblood	blood
45	chr19:42393400-42400800	Genic enhancers	Primary T helper memory cells from peripheral blood 2	blood
46	chr19:42393400-42400800	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
47	chr19:42393400-42404600	Genic enhancers	Primary T helper cells PMA-I stimulated	--
48	chr19:42393400-42413600	Strong transcription	Thymus	Thymus
49	chr19:42393800-42401800	Weak transcription	NH-A	brain
50	chr19:42393800-42402200	Genic enhancers	Primary T cells from cord blood	blood

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