Variant report

Variant	rs8107383
Chromosome Location	chr19:52692296-52692297
allele	A/G
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	MXI1	chr19:52692258-52693773	Hela-S3	cervix:	n/a	n/a
2	MAZ	chr19:52692230-52693947	GM12878	blood:	n/a	chr19:52693618-52693628 chr19:52693289-52693299 chr19:52693254-52693263
3	NFIC	chr19:52692271-52693629	ECC-1	luminal epithelium:	n/a	n/a
4	POLR2A	chr19:52692067-52694881	GM12891	blood:	n/a	n/a
5	TBP	chr19:52692269-52693507	Hela-S3	cervix:	n/a	n/a
6	EP300	chr19:52692152-52692660	T-47D	breast:	n/a	n/a
7	GATA3	chr19:52692198-52692635	SH-SY5Y	brain:	n/a	chr19:52692398-52692410
8	SIN3AK20	chr19:52692117-52694086	MCF-7	breast:	n/a	n/a
9	POLR2A	chr19:52692031-52693988	H1-hESC	embryonic stem cell:	n/a	n/a
10	MTA3	chr19:52692265-52694253	GM12878	blood:	n/a	n/a
11	MAZ	chr19:52691865-52695094	IMR90	lung:	n/a	chr19:52693618-52693628 chr19:52693289-52693299 chr19:52693254-52693263
12	TBP	chr19:52692058-52694098	H1-hESC	embryonic stem cell:	n/a	n/a
13	NRF1	chr19:52692079-52694626	SK-N-SH	brain:	n/a	chr19:52693665-52693674 chr19:52692927-52692938 chr19:52692927-52692938 chr19:52692927-52692941 chr19:52693082-52693089 chr19:52692883-52692894
14	REST	chr19:52692168-52694507	H1-neurons	neurons:	n/a	chr19:52693675-52693689 chr19:52693669-52693689 chr19:52693672-52693685 chr19:52693669-52693689
15	POLR2A	chr19:52692178-52695116	H1-hESC	embryonic stem cell:	n/a	n/a
16	CTCF	chr19:52692260-52692410	HMEC	breast:	n/a	n/a
17	GATA2	chr19:52691877-52693850	SH-SY5Y	brain:	n/a	chr19:52693555-52693562 chr19:52692398-52692410 chr19:52693554-52693564 chr19:52693555-52693564 chr19:52693555-52693562 chr19:52693555-52693562
18	BACH1	chr19:52692276-52692354	K562	blood:	n/a	n/a
19	POLR2A	chr19:52691879-52695550	GM12878	blood:	n/a	n/a
20	TCF12	chr19:52692211-52694144	A549	lung:	n/a	n/a
21	TCF12	chr19:52692153-52692497	H1-hESC	embryonic stem cell:	n/a	n/a
22	RELA	chr19:52692209-52694217	GM15510	blood:	n/a	n/a
23	HA-E2F1	chr19:52692160-52693932	MCF-7	breast:	n/a	chr19:52693746-52693755
24	SMC3	chr19:52692236-52693658	Hela-S3	cervix:	n/a	n/a
25	MAX	chr19:52692151-52692672	H1-hESC	embryonic stem cell:	n/a	n/a
26	CEBPB	chr19:52692145-52693668	Hela-S3	cervix:	n/a	chr19:52692996-52693004
27	RCOR1	chr19:52692205-52693513	Hela-S3	cervix:	n/a	n/a
28	MTA3	chr19:52692285-52692700	GM12878	blood:	n/a	n/a
29	POLR2A	chr19:52692187-52692319	HUVEC	blood vessel:	n/a	n/a
30	POLR2A	chr19:52691751-52694908	SK-N-MC	brain:	n/a	n/a
31	POLR2A	chr19:52692049-52694455	Hela-S3	cervix:	n/a	n/a
32	POLR2A	chr19:52692172-52694154	MCF10A-Er-Src	breast:	n/a	n/a
33	HCFC1	chr19:52692080-52693988	Hela-S3	cervix:	n/a	n/a
34	TCF12	chr19:52692259-52694008	ECC-1	luminal epithelium:	n/a	n/a
35	MXI1	chr19:52691658-52695097	SK-N-SH	brain:	n/a	n/a
36	ESR1	chr19:52692276-52692521	T-47D	breast:	n/a	n/a
37	FOXA1	chr19:52692283-52692536	T-47D	breast:	n/a	n/a
38	GATA3	chr19:52692171-52692603	T-47D	breast:	n/a	chr19:52692398-52692410
39	GTF2F1	chr19:52692111-52692376	H1-hESC	embryonic stem cell:	n/a	n/a
40	ZNF143	chr19:52692028-52692422	H1-hESC	embryonic stem cell:	n/a	n/a
41	CHD1	chr19:52692295-52692974	GM12878	blood:	n/a	n/a
42	TEAD4	chr19:52692105-52692566	H1-hESC	embryonic stem cell:	n/a	n/a
43	SREBP2	chr19:52692076-52695013	GM12878	blood:	n/a	n/a
44	POLR2A	chr19:52692021-52693956	GM12878	blood:	n/a	n/a
45	RAD21	chr19:52692131-52692977	H1-hESC	embryonic stem cell:	n/a	n/a
46	GTF2F1	chr19:52692126-52693731	Hela-S3	cervix:	n/a	n/a
47	POLR2A	chr19:52692276-52694524	GM12892	blood:	n/a	n/a
48	GATA3	chr19:52692163-52692638	T-47D	breast:	n/a	chr19:52692398-52692410
49	MAX	chr19:52692198-52693809	Hela-S3	cervix:	n/a	chr19:52693618-52693628 chr19:52693289-52693299 chr19:52693254-52693263
50	ATF2	chr19:52692046-52693003	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:52641405..52644253-chr19:52691691..52696539,6	MCF-7	breast:
2	chr19:52598726..52600984-chr19:52691577..52693709,2	MCF-7	breast:
3	chr19:52597423..52599077-chr19:52692134..52694986,2	K562	blood:
4	chr19:52672904..52675094-chr19:52691087..52692994,2	K562	blood:
5	chr19:52641479..52644491-chr19:52690575..52695402,7	MCF-7	breast:
6	chr19:52671404..52675593-chr19:52690586..52694996,6	MCF-7	breast:
7	chr19:52690613..52692739-chr19:52771560..52774323,2	K562	blood:
8	chr19:52691967..52694543-chr19:52715939..52718199,3	MCF-7	breast:
9	chr19:52691998..52694919-chr19:53605403..53608321,3	K562	blood:
10	chr19:52677704..52680219-chr19:52691425..52693169,2	MCF-7	breast:

Variant related genes	Relation type
PPP2R1A	TF binding region
ENSG00000196267	Chromatin interaction
ENSG00000256087	Chromatin interaction
ENSG00000170949	Chromatin interaction
ENSG00000105568	Chromatin interaction
ENSG00000196214	Chromatin interaction
ENSG00000267927	Chromatin interaction
ENSG00000267827	Chromatin interaction
ENSG00000204611	Chromatin interaction
ENSG00000197608	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10520481	0.87[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap]
rs13344871	1.00[JPT][hapmap]
rs16983537	0.87[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs16983625	0.87[CEU][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap]
rs16983630	0.87[CEU][hapmap];1.00[JPT][hapmap]
rs2002322	1.00[JPT][hapmap]
rs2560903	1.00[JPT][hapmap]
rs2657929	1.00[JPT][hapmap]
rs2657932	1.00[JPT][hapmap]
rs61196205	0.85[EUR][1000 genomes]
rs61380660	0.83[EUR][1000 genomes]
rs62109201	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62109202	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62109205	1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs62109247	0.81[EUR][1000 genomes]
rs7249460	1.00[JPT][hapmap]
rs7251497	0.87[CEU][hapmap];1.00[JPT][hapmap]
rs7251605	1.00[JPT][hapmap]
rs73575024	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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	esv3366000	chr19:52491073-52842946	Strong transcription ZNF genes & repeats Weak transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
3	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
4	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
5	nsv580007	chr19:52660279-52693277	Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
6	nsv1059417	chr19:52662380-52703801	Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
7	esv2760529	chr19:52662380-52703813	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:52691600-52694600	Active TSS	iPS-20b Cell Line	embryonic stem cell
2	chr19:52691800-52692400	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
3	chr19:52691800-52692400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr19:52691800-52692400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr19:52691800-52692400	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
6	chr19:52691800-52692400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
7	chr19:52691800-52692400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
8	chr19:52691800-52692400	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr19:52691800-52692400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr19:52691800-52692400	Flanking Active TSS	Liver	Liver
11	chr19:52691800-52692400	Flanking Active TSS	Brain Anterior Caudate	brain
12	chr19:52691800-52692400	Flanking Active TSS	Brain Germinal Matrix	brain
13	chr19:52691800-52692400	Flanking Active TSS	Rectal Smooth Muscle	rectum
14	chr19:52691800-52692400	ZNF genes & repeats	A549	lung
15	chr19:52691800-52692400	Flanking Active TSS	Hela-S3	cervix
16	chr19:52691800-52692400	Flanking Active TSS	HMEC	breast
17	chr19:52691800-52692600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr19:52691800-52692600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr19:52691800-52692600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
20	chr19:52691800-52692600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr19:52691800-52692600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr19:52691800-52692600	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
23	chr19:52691800-52692600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
24	chr19:52691800-52692600	Enhancers	Spleen	Spleen
25	chr19:52691800-52692600	Flanking Active TSS	Dnd41	blood
26	chr19:52691800-52692600	Flanking Active TSS	NHEK	skin
27	chr19:52691800-52694400	Active TSS	HUES6 Cell Line	embryonic stem cell
28	chr19:52691800-52694600	Active TSS	ES-I3 Cell Line	embryonic stem cell
29	chr19:52691800-52694600	Active TSS	HUES64 Cell Line	embryonic stem cell
30	chr19:52692000-52692400	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr19:52692000-52692400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr19:52692000-52692400	Enhancers	Primary neutrophils fromperipheralblood	blood
33	chr19:52692000-52692400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
34	chr19:52692000-52692400	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr19:52692000-52692400	Flanking Active TSS	Brain Angular Gyrus	brain
36	chr19:52692000-52692400	Flanking Active TSS	Brain Cingulate Gyrus	brain
37	chr19:52692000-52692400	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
38	chr19:52692000-52692400	Flanking Active TSS	Brain Substantia Nigra	brain
39	chr19:52692000-52692400	Flanking Active TSS	Duodenum Mucosa	Duodenum
40	chr19:52692000-52692400	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
41	chr19:52692000-52692400	Flanking Active TSS	Fetal Brain Male	brain
42	chr19:52692000-52692400	Flanking Active TSS	Fetal Brain Female	brain
43	chr19:52692000-52692400	Flanking Active TSS	Fetal Heart	heart
44	chr19:52692000-52692400	Flanking Active TSS	Fetal Kidney	kidney
45	chr19:52692000-52692400	Flanking Active TSS	Fetal Lung	lung
46	chr19:52692000-52692400	Flanking Active TSS	Fetal Stomach	stomach
47	chr19:52692000-52692400	Flanking Active TSS	Placenta Amnion	Placenta Amnion
48	chr19:52692000-52692400	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
49	chr19:52692000-52692400	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
50	chr19:52692000-52692400	Flanking Active TSS	Right Ventricle	heart

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