Variant report

Variant	esv20520
Chromosome Location	chr19:56686719-56688658
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:8)
CpG islands
(count:428)
Chromatin interactive
region (count:2)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:8 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr19:56687403-56687437	Lung_OC	lung:	n/a	n/a
2	POLR2A	chr19:56688476-56688487	MCF-7	breast:	n/a	n/a
3	POLR2A	chr19:56688412-56688454	MCF-7	breast:	n/a	n/a
4	REST	chr19:56687362-56688032	PANC-1	pancreas:	n/a	n/a
5	SRF	chr19:56687513-56687741	GM12878	blood:	n/a	n/a
6	TBL1XR1	chr19:56687039-56687093	K562	blood:	n/a	n/a
7	TCF3	chr19:56687530-56687910	GM12878	blood:	n/a	n/a
8	USF1	chr19:56686686-56686821	HepG2	liver:	n/a	chr19:56686733-56686744

(count:428 , 50 per page) page: 1 2 3 4 5 6 7 ... 9

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr19:56687388-56687438	LNCaP	prostate:	n/a
2	chr19:56687388-56687438	LNCaP	prostate:	n/a
3	chr19:56688423-56688473	BE2_C	brain:	n/a
4	chr19:56687199-56687249	HCT-116	colon:	n/a
5	chr19:56686707-56686757	GM12891	blood:	n/a
6	chr19:56688423-56688473	AoSMC	blood vessel:	n/a
7	chr19:56687197-56687247	HRPEpiC	eye:	n/a
8	chr19:56687388-56687438	PFSK-1	brain:	n/a
9	chr19:56688423-56688473	Caco-2	colon:	n/a
10	chr19:56688423-56688473	HRPEpiC	eye:	n/a
11	chr19:56687364-56687414	HCF	heart:	n/a
12	chr19:56688423-56688473	HPAEpiC	pulmonary alveolar:	n/a
13	chr19:56687199-56687249	Caco-2	colon:	n/a
14	chr19:56687197-56687247	HCM	heart:	n/a
15	chr19:56686707-56686757	HEEpiC	esophagus:	n/a
16	chr19:56688439-56688489	Jurkat	blood:	n/a
17	chr19:56688439-56688489	NB4	blood:	n/a
18	chr19:56688423-56688473	HUVEC	blood vessel:	n/a
19	chr19:56687197-56687247	BE2_C	brain:	n/a
20	chr19:56687388-56687438	AG09309	skin:	n/a
21	chr19:56686707-56686757	NT2-D1	testis:	n/a
22	chr19:56687364-56687414	HL-60	blood:	n/a
23	chr19:56687364-56687414	A549	lung:	n/a
24	chr19:56687364-56687414	AG04449	skin:	fetal
25	chr19:56686707-56686757	AG04449	skin:	fetal
26	chr19:56687197-56687247	ProgFib	skin:	n/a
27	chr19:56687364-56687414	BE2_C	brain:	n/a
28	chr19:56688423-56688473	MCF-7	breast:	n/a
29	chr19:56687388-56687438	AG10803	skin:	n/a
30	chr19:56688439-56688489	NH-A	brain:	n/a
31	chr19:56688439-56688489	SKMC	muscle:	n/a
32	chr19:56688439-56688489	HRPEpiC	eye:	n/a
33	chr19:56687364-56687414	SK-N-MC	brain:	n/a
34	chr19:56688439-56688489	AG04450	lung:	fetal
35	chr19:56687364-56687414	GM06990	blood:	n/a
36	chr19:56687388-56687438	HCPEpiC	choroid plexus:	n/a
37	chr19:56687388-56687438	NT2-D1	testis:	n/a
38	chr19:56688439-56688489	SAEC	small airway:	n/a
39	chr19:56687388-56687438	HMEC	breast:	n/a
40	chr19:56686707-56686757	AoSMC	blood vessel:	n/a
41	chr19:56688423-56688473	PANC-1	pancreas:	n/a
42	chr19:56687197-56687247	HRE	kidney:	n/a
43	chr19:56687197-56687247	AG04449	skin:	fetal
44	chr19:56688439-56688489	HNPCEpiC	eye:	n/a
45	chr19:56687388-56687438	AG09319	gingival:	n/a
46	chr19:56688439-56688489	AG09319	gingival:	n/a
47	chr19:56687388-56687438	MCF10A-Er-Src	breast:	n/a
48	chr19:56687364-56687414	Jurkat	blood:	n/a
49	chr19:56686707-56686757	SK-N-SH_RA	brain:	n/a
50	chr19:56687197-56687247	NH-A	brain:	n/a

(count:2 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:56688624..56690608-chr19:56692405..56694978,2	K562	blood:
2	chr19:56651843..56653969-chr19:56684721..56686741,2	MCF-7	breast:

No data

Variant related genes	Relation type
GALP	TF binding region
GALP	CpG island
ENSG00000167685	chromatin interactions

Extended variants
information (count: 138 )
Associated
traits (count: 69 )

Variant overlapped rSNPs/rCNVs (count:138 , 50 per page) page: 1 2 3

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs193151205	chr19:56686734-56686735	Enhancers Weak transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
2	rs185655234	chr19:56686740-56686741	Enhancers Weak transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
3	rs274167	chr19:56686756-56686757	Enhancers Weak transcription Bivalent Enhancer	TF binding region CpG island	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
4	rs112068161	chr19:56686796-56686797	Enhancers Weak transcription Bivalent Enhancer	TF binding region	1 gene(s)	Overlapped CNVs	n/a
5	rs274168	chr19:56686801-56686802	Enhancers Bivalent Enhancer Weak transcription	TF binding region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
6	rs274169	chr19:56686886-56686887	Enhancers Bivalent Enhancer Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
7	rs3810336	chr19:56686894-56686895	Enhancers Bivalent Enhancer Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
8	rs143116332	chr19:56686897-56686898	Enhancers Bivalent Enhancer Weak transcription	n/a	n/a	Overlapped CNVs	n/a
9	rs274170	chr19:56686953-56686954	Enhancers Bivalent Enhancer Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
10	rs543976745	chr19:56686964-56686965	Enhancers Bivalent Enhancer Weak transcription	n/a	n/a	Overlapped CNVs	n/a
11	rs553435257	chr19:56687030-56687031	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription	n/a	n/a	Overlapped CNVs	n/a
12	rs529934576	chr19:56687063-56687064	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
13	rs189314558	chr19:56687068-56687069	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
14	rs77916251	chr19:56687077-56687078	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
15	rs531971716	chr19:56687091-56687092	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
16	rs187987	chr19:56687106-56687107	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription	n/a	n/a	Overlapped CNVs	n/a
17	rs192648029	chr19:56687109-56687110	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription	n/a	n/a	Overlapped CNVs	n/a
18	rs532057421	chr19:56687167-56687168	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription	n/a	n/a	Overlapped CNVs	n/a
19	rs548931520	chr19:56687174-56687175	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription	n/a	n/a	Overlapped CNVs	n/a
20	rs111587076	chr19:56687186-56687187	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription	n/a	n/a	Overlapped CNVs	n/a
21	rs534448287	chr19:56687202-56687203	Enhancers Weak transcription Bivalent Enhancer	CpG island	1 gene(s)	Overlapped CNVs	n/a
22	rs547568670	chr19:56687220-56687221	Enhancers Weak transcription Bivalent Enhancer	CpG island	1 gene(s)	Overlapped CNVs	n/a
23	rs184258475	chr19:56687233-56687234	Enhancers Weak transcription Bivalent Enhancer	CpG island	1 gene(s)	Overlapped CNVs	n/a
24	rs188517112	chr19:56687294-56687295	Enhancers Weak transcription Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
25	rs77226233	chr19:56687307-56687308	Enhancers Weak transcription Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
26	rs573246029	chr19:56687316-56687317	Enhancers Weak transcription Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
27	rs181607361	chr19:56687320-56687321	Enhancers Weak transcription Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
28	rs3810339	chr19:56687321-56687322	Enhancers Weak transcription Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
29	rs553785439	chr19:56687330-56687331	Enhancers Weak transcription Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
30	rs574537189	chr19:56687348-56687349	Enhancers Weak transcription Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
31	rs540431814	chr19:56687364-56687365	Enhancers Weak transcription Bivalent Enhancer	TF binding region CpG island	1 gene(s)	Overlapped CNVs	n/a
32	rs146668117	chr19:56687365-56687366	Enhancers Weak transcription Bivalent Enhancer	TF binding region CpG island	1 gene(s)	Overlapped CNVs	n/a
33	rs72490747	chr19:56687381-56687382	Enhancers Weak transcription Bivalent Enhancer	TF binding region CpG island	1 gene(s)	Overlapped CNVs	n/a
34	rs542249616	chr19:56687388-56687389	Enhancers Weak transcription Bivalent Enhancer	TF binding region CpG island	1 gene(s)	Overlapped CNVs	n/a
35	rs545779290	chr19:56687389-56687390	Enhancers Weak transcription Bivalent Enhancer	TF binding region CpG island	1 gene(s)	Overlapped CNVs	n/a
36	rs73934756	chr19:56687427-56687428	Enhancers Flanking Active TSS Weak transcription	TF binding region CpG island	1 gene(s)	Overlapped CNVs	n/a
37	rs531358894	chr19:56687447-56687448	Enhancers Flanking Active TSS Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
38	rs143816373	chr19:56687456-56687457	Enhancers Flanking Active TSS Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
39	rs34947076	chr19:56687462-56687463	Enhancers Flanking Active TSS Weak transcription	TF binding region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
40	rs372065678	chr19:56687467-56687468	Enhancers Flanking Active TSS Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
41	rs527843238	chr19:56687469-56687470	Enhancers Flanking Active TSS Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
42	rs374408323	chr19:56687477-56687478	Enhancers Flanking Active TSS Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
43	rs547974558	chr19:56687478-56687479	Enhancers Flanking Active TSS Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
44	rs368158612	chr19:56687506-56687507	Enhancers Flanking Active TSS Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
45	rs35943411	chr19:56687511-56687512	Enhancers Flanking Active TSS Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
46	rs539939720	chr19:56687528-56687529	Enhancers Flanking Active TSS Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
47	rs549897001	chr19:56687545-56687546	Enhancers Flanking Active TSS Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
48	rs569693567	chr19:56687554-56687555	Enhancers Flanking Active TSS Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
49	rs35077371	chr19:56687556-56687557	Enhancers Flanking Active TSS Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
50	rs535504367	chr19:56687563-56687564	Enhancers Flanking Active TSS Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:69)

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
T-cell prolymphocytic leukemia	19278963	CNVD
Prostate cancer	18632612	CNVD
Ductal carcinoma	22052326	CNVD
Congenital nephrotic syndrome	18421352	CNVD
Astrocytoma	17934521	CNVD
Leukemia	17361228	CNVD
Adenoid cystic carcinoma	17372589	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
Adenoid cystic carcinoma	18698036	CNVD
Salivary gland adenoid cystic carcinoma	17545515	CNVD
Breast cancer	16608533	CNVD
Neuroblastoma	18923191	CNVD
Chordoma	18071362	CNVD
Urothelial carcinoma	21177765	CNVD
Metanephric adenoma	20802469	CNVD
Acute myeloid leukemia	16864856	CNVD
Bladder cancer	21909424	CNVD
Medulloblastoma	16783165	CNVD
Acute myeloid leukemia	20729466	CNVD
Ovarian cancer	22174824	CNVD
Multiple myeloma	16616336	CNVD
Acute lymphoblastic leukemia	21339820	CNVD
Wilms tumour	21544195	CNVD
low-grade B-cell lymphoma tumor	18367492	CNVD
Congenital anomalies of the kidney and urinary tract	18852474	CNVD
Glioblastoma multiforme	17002787	CNVD
Cervical cancer	21062161	CNVD
Primary central nervous system lymphoma	21088137	CNVD
Prostate cancer	16573809	CNVD
small cell lung cancer	20016488	CNVD
Acute lymphoblastic leukemia	17690704	CNVD
T-cell prolymphocytic leukemia	17713554	CNVD
Lung cancer	18438408	CNVD
Colorectal cancer	16272173	CNVD
Ovarian cancer	21781307	CNVD
Neuroblastoma	20406844	CNVD
Breast cancer	21785460	CNVD
Myelofibrosis	22110671	CNVD
T-cell acute lymphoblastic leukemia	19406988	CNVD
Alzheimer''s disease	22166940	CNVD
Heart disease	21282601	CNVD
Diffuse large b-cell lymphoma	18287131	CNVD
Glioblastoma multiforme	21922591	CNVD
Non-syndromic sensorineural hearing loss	18496225	CNVD
Basal cell lymphoma	19029149	CNVD
Diffuse large b-cell lymphoma	19029149	CNVD
Breast cancer	20409316	CNVD
Non-syndromic sensorineural hearing loss	17289997	CNVD
Non-syndromic sensorineural hearing loss	17122850	CNVD
Breast cancer	22522925	CNVD
Pancreatic cancer	17952125	CNVD

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:56673000-56690000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr19:56682000-56687000	Weak transcription	Spleen	Spleen
3	chr19:56685400-56687200	Enhancers	K562	blood
4	chr19:56685600-56687400	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
5	chr19:56685600-56687600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr19:56685600-56688600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr19:56685800-56686800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr19:56685800-56688000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr19:56686400-56687000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr19:56686400-56687200	Bivalent Enhancer	HepG2	liver
11	chr19:56686600-56688200	Enhancers	Liver	Liver
12	chr19:56686600-56688400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr19:56686800-56687200	Enhancers	H1 Cell Line	embryonic stem cell
14	chr19:56686800-56687200	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
15	chr19:56686800-56687400	Enhancers	Brain Germinal Matrix	brain
16	chr19:56686800-56688000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
17	chr19:56687000-56687200	Flanking Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr19:56687000-56687200	Enhancers	Spleen	Spleen
19	chr19:56687000-56687400	Enhancers	HUES64 Cell Line	embryonic stem cell
20	chr19:56687200-56687400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr19:56687400-56687600	Flanking Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr19:56687400-56687600	Flanking Active TSS	Brain Germinal Matrix	brain
23	chr19:56687600-56688000	Active TSS	Brain Germinal Matrix	brain
24	chr19:56687600-56688600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr19:56688000-56688200	Flanking Active TSS	Brain Germinal Matrix	brain
26	chr19:56688200-56689200	Weak transcription	Liver	Liver
27	chr19:56688600-56702400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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