Variant report

Variant	rs73581129
Chromosome Location	chr19:52873239-52873240
allele	C/T
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	POLR2A	chr19:52872752-52873762	HUVEC	blood vessel:	n/a	n/a
2	STAT5A	chr19:52873031-52873493	GM12878	blood:	n/a	chr19:52873031-52873038
3	POLR2A	chr19:52873022-52873416	GM15510	blood:	n/a	n/a
4	TAF1	chr19:52872982-52873806	H1-hESC	embryonic stem cell:	n/a	n/a
5	POLR2A	chr19:52872990-52873681	GM12878	blood:	n/a	n/a
6	YY1	chr19:52873021-52873360	GM12878	blood:	n/a	n/a
7	TAF1	chr19:52873014-52873682	H1-neurons	neurons:	n/a	n/a
8	JUND	chr19:52872899-52873369	H1-hESC	embryonic stem cell:	n/a	n/a
9	MAX	chr19:52872650-52873385	H1-hESC	embryonic stem cell:	n/a	n/a
10	TBP	chr19:52872964-52873635	H1-hESC	embryonic stem cell:	n/a	n/a
11	POLR2A	chr19:52872945-52873618	HUVEC	blood vessel:	n/a	n/a
12	CREB1	chr19:52872963-52873416	GM12878	blood:	n/a	n/a
13	TAF1	chr19:52873096-52873391	GM12891	blood:	n/a	n/a
14	KAP1	chr19:52872949-52873663	HEK293	kidney:	n/a	n/a
15	RUNX3	chr19:52872762-52873593	GM12878	blood:	n/a	n/a
16	MTA3	chr19:52873199-52873800	GM12878	blood:	n/a	n/a
17	GABPA	chr19:52872906-52873400	HL-60	blood:	n/a	n/a
18	GABPA	chr19:52872990-52873702	MCF-7	breast:	n/a	n/a
19	TBL1XR1	chr19:52872897-52873369	GM12878	blood:	n/a	n/a
20	ELK1	chr19:52873079-52873375	GM12878	blood:	n/a	n/a
21	POLR2A	chr19:52872927-52873670	GM19193	blood:	n/a	n/a
22	POLR2A	chr19:52872946-52873617	SK-N-SH	brain:	n/a	n/a
23	TAF7	chr19:52873015-52873428	H1-hESC	embryonic stem cell:	n/a	n/a
24	POLR2A	chr19:52872886-52873673	GM19099	blood:	n/a	n/a
25	POLR2A	chr19:52873038-52873343	Gliobla	brain:	n/a	n/a
26	POLR2A	chr19:52872801-52873632	HUVEC	blood vessel:	n/a	n/a
27	POLR2A	chr19:52872972-52873638	GM12891	blood:	n/a	n/a
28	POLR2A	chr19:52872944-52873740	H1-neurons	neurons:	n/a	n/a
29	IRF3	chr19:52873199-52873394	GM12878	blood:	n/a	n/a
30	ELF1	chr19:52872775-52873661	SK-N-SH	brain:	n/a	chr19:52873187-52873198 chr19:52873188-52873197 chr19:52873185-52873198
31	GABPA	chr19:52872839-52873644	MCF-7	breast:	n/a	n/a
32	POLR2A	chr19:52872889-52873735	GM12891	blood:	n/a	n/a
33	EP300	chr19:52873136-52873641	GM12878	blood:	n/a	n/a
34	MAX	chr19:52872769-52873354	H1-hESC	embryonic stem cell:	n/a	n/a
35	POLR2A	chr19:52872974-52873720	GM12891	blood:	n/a	n/a
36	GABPA	chr19:52873060-52873266	A549	lung:	n/a	n/a
37	ETS1	chr19:52872915-52873396	GM12878	blood:	n/a	n/a
38	GATA2	chr19:52873045-52873554	HUVEC	blood vessel:	n/a	n/a
39	POLR2A	chr19:52872886-52873777	GM12878	blood:	n/a	n/a
40	ELF1	chr19:52872977-52873387	MCF-7	breast:	n/a	chr19:52873187-52873198 chr19:52873188-52873197 chr19:52873185-52873198
41	EP300	chr19:52873044-52873269	SK-N-SH_RA	brain:	n/a	n/a
42	POLR2A	chr19:52872814-52873738	GM12878	blood:	n/a	n/a
43	MAZ	chr19:52872920-52873730	GM12878	blood:	n/a	n/a
44	MAX	chr19:52872765-52873525	SK-N-SH	brain:	n/a	n/a
45	POLR2A	chr19:52872935-52873798	GM12878	blood:	n/a	n/a
46	GATA3	chr19:52873225-52873866	SH-SY5Y	brain:	n/a	n/a
47	RCOR1	chr19:52873149-52873317	GM12878	blood:	n/a	n/a
48	POLR2A	chr19:52872794-52873657	SK-N-MC	brain:	n/a	n/a
49	CHD1	chr19:52873085-52873535	GM12878	blood:	n/a	n/a
50	NRF1	chr19:52872785-52873961	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:52771473..52773658-chr19:52872286..52874915,2	MCF-7	breast:

Variant related genes	Relation type
ZNF880	TF binding region
ENSG00000196214	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs10401299	1.00[AMR][1000 genomes]
rs10406085	1.00[AMR][1000 genomes]
rs10412822	1.00[AMR][1000 genomes]
rs10418954	1.00[AMR][1000 genomes]
rs10420125	1.00[AMR][1000 genomes]
rs10420812	1.00[AMR][1000 genomes]
rs10423371	1.00[AMR][1000 genomes]
rs10423818	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60323875	1.00[AMR][1000 genomes]
rs73581108	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1065410	chr19:52103914-52889530	Genic enhancers Enhancers ZNF genes & repeats Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	596 gene(s)	inside rSNPs	diseases
2	nsv1066015	chr19:52502213-52890308	Flanking Active TSS ZNF genes & repeats Enhancers Weak transcription Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	nsv544059	chr19:52502213-52890308	Active TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
4	nsv833873	chr19:52788939-52937281	Weak transcription Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
5	nsv1066537	chr19:52794424-53044977	Active TSS ZNF genes & repeats Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
6	nsv544060	chr19:52794424-53044977	ZNF genes & repeats Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
7	esv3401193	chr19:52818960-52909749	ZNF genes & repeats Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
8	nsv912300	chr19:52832830-52928039	Active TSS Strong transcription ZNF genes & repeats Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
9	nsv912301	chr19:52835210-52914233	ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
10	nsv912302	chr19:52859828-52928039	Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Weak transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
11	nsv2536	chr19:52869457-52902064	Flanking Active TSS Enhancers ZNF genes & repeats Weak transcription Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:52865200-52875400	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr19:52866600-52875400	ZNF genes & repeats	Liver	Liver
3	chr19:52871200-52876400	Weak transcription	Dnd41	blood
4	chr19:52872400-52873600	Active TSS	Monocytes-CD14+_RO01746	blood
5	chr19:52872400-52874000	Active TSS	Duodenum Smooth Muscle	Duodenum
6	chr19:52872600-52873400	Active TSS	Primary T cells from cord blood	blood
7	chr19:52872600-52873800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr19:52872600-52873800	Active TSS	Fetal Brain Female	brain
9	chr19:52872600-52873800	Active TSS	Right Ventricle	heart
10	chr19:52872600-52874000	Active TSS	Breast Myoepithelial Primary Cells	Breast
11	chr19:52872600-52874000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr19:52872600-52874000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr19:52872600-52874000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
14	chr19:52872600-52874000	Active TSS	Duodenum Mucosa	Duodenum
15	chr19:52872600-52874000	Active TSS	Fetal Adrenal Gland	Adrenal Gland
16	chr19:52872600-52874000	Active TSS	Fetal Intestine Small	intestine
17	chr19:52872600-52874000	Active TSS	Fetal Muscle Trunk	muscle
18	chr19:52872600-52874000	Active TSS	Fetal Muscle Leg	muscle
19	chr19:52872600-52874000	Active TSS	Fetal Stomach	stomach
20	chr19:52872600-52874000	Active TSS	Right Atrium	heart
21	chr19:52872600-52874000	Active TSS	Thymus	Thymus
22	chr19:52872600-52874200	Active TSS	HUES48 Cell Line	embryonic stem cell
23	chr19:52872600-52874400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr19:52872600-52874400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr19:52872600-52874400	Active TSS	Fetal Kidney	kidney
26	chr19:52872600-52874800	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr19:52872800-52873400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr19:52872800-52873400	Active TSS	Primary T helper cells PMA-I stimulated	--
29	chr19:52872800-52873400	Active TSS	Pancreatic Islets	Pancreatic Islet
30	chr19:52872800-52873400	Active TSS	HUVEC	blood vessel
31	chr19:52872800-52873600	Active TSS	Primary B cells from cord blood	blood
32	chr19:52872800-52873600	Active TSS	Primary hematopoietic stem cells short term culture	blood
33	chr19:52872800-52873600	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
34	chr19:52872800-52873600	Active TSS	Primary T helper naive cells from peripheral blood	blood
35	chr19:52872800-52873600	Active TSS	Primary T killer naive cells fromperipheralblood	blood
36	chr19:52872800-52873600	Active TSS	Primary T killer memory cells from peripheral blood	blood
37	chr19:52872800-52873600	Active TSS	Colonic Mucosa	Colon
38	chr19:52872800-52873600	Active TSS	Fetal Brain Male	brain
39	chr19:52872800-52873800	Active TSS	iPS-15b Cell Line	embryonic stem cell
40	chr19:52872800-52873800	Active TSS	iPS-18 Cell Line	embryonic stem cell
41	chr19:52872800-52873800	ZNF genes & repeats	Primary mononuclear cells fromperipheralblood	Blood
42	chr19:52872800-52873800	Active TSS	Aorta	Aorta
43	chr19:52872800-52873800	Active TSS	Brain Angular Gyrus	brain
44	chr19:52872800-52873800	Active TSS	Brain Substantia Nigra	brain
45	chr19:52872800-52873800	Active TSS	Colon Smooth Muscle	Colon
46	chr19:52872800-52873800	Active TSS	Gastric	stomach
47	chr19:52872800-52873800	ZNF genes & repeats	Lung	lung
48	chr19:52872800-52873800	Active TSS	Stomach Mucosa	stomach
49	chr19:52872800-52874000	Active TSS	H1 Cell Line	embryonic stem cell
50	chr19:52872800-52874000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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