Variant report

Variant	rs409803
Chromosome Location	chr3:52443280-52443281
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	RCOR1	chr3:52443055-52444488	IMR90	lung:	n/a	n/a
2	MAZ	chr3:52443249-52445513	IMR90	lung:	n/a	n/a
3	MXI1	chr3:52443027-52445926	SK-N-SH	brain:	n/a	n/a
4	MTA3	chr3:52442995-52444180	GM12878	blood:	n/a	n/a
5	ESRRA	chr3:52442736-52445785	GM12878	blood:	n/a	chr3:52444629-52444645 chr3:52443225-52443237 chr3:52443981-52443994 chr3:52444631-52444641 chr3:52445485-52445504
6	REST	chr3:52443152-52446007	H1-neurons	neurons:	n/a	chr3:52443163-52443176 chr3:52443304-52443317 chr3:52444795-52444805

No.	Distal block	Cell Line	Cell type
1	chr3:52441032..52443343-chr3:52444895..52446688,2	MCF-7	breast:
2	chr3:52420801..52424667-chr3:52442297..52446214,5	K562	blood:
3	chr3:52442610..52445343-chr3:52803282..52805357,2	K562	blood:
4	chr3:52324588..52327004-chr3:52442941..52444727,2	MCF-7	breast:
5	chr3:52311359..52313564-chr3:52443173..52445594,2	MCF-7	breast:
6	chr3:52015943..52018006-chr3:52443224..52445803,2	K562	blood:
7	chr3:52271478..52274801-chr3:52443057..52446273,4	K562	blood:
8	chr3:52442891..52445847-chr3:52570573..52572369,2	K562	blood:
9	chr3:52272619..52275147-chr3:52443057..52446254,5	K562	blood:
10	chr3:52443115..52446014-chr3:52718098..52719635,2	K562	blood:

Variant related genes	Relation type
BAP1	TF binding region
PHF7	TF binding region
ENSG00000163939	Chromatin interaction
ENSG00000168237	Chromatin interaction
ENSG00000168273	Chromatin interaction
ENSG00000243989	Chromatin interaction
ENSG00000114904	Chromatin interaction
ENSG00000114779	Chromatin interaction
ENSG00000114841	Chromatin interaction
ENSG00000247596	Chromatin interaction
ENSG00000239732	Chromatin interaction
ENSG00000010318	Chromatin interaction
ENSG00000243224	Chromatin interaction
ENSG00000164091	Chromatin interaction

Extended variants
information (count: 127 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:120)

rs_ID	r²[population]
rs1011062	1.00[JPT][hapmap];0.82[MEX][hapmap];0.85[TSI][hapmap];0.81[EUR][1000 genomes]
rs1011063	1.00[JPT][hapmap]
rs1011064	1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs1035002	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1035003	0.81[EUR][1000 genomes]
rs1077142	1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs10865972	0.82[CEU][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11707864	1.00[JPT][hapmap]
rs11707931	1.00[JPT][hapmap]
rs11709658	1.00[JPT][hapmap]
rs11711934	1.00[JPT][hapmap]
rs11714402	1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs11716017	1.00[JPT][hapmap]
rs11718125	1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs11721286	1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs123598	1.00[JPT][hapmap];0.82[MEX][hapmap];0.92[TSI][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs123602	0.85[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs123603	1.00[ASW][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.95[MKK][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];0.88[EUR][1000 genomes]
rs13059674	1.00[JPT][hapmap]
rs13060192	1.00[JPT][hapmap];0.82[MEX][hapmap];0.85[TSI][hapmap]
rs13065677	0.83[AMR][1000 genomes]
rs13071708	1.00[JPT][hapmap];0.82[MEX][hapmap];0.85[TSI][hapmap];0.83[AMR][1000 genomes]
rs13074649	0.81[EUR][1000 genomes]
rs13075370	1.00[JPT][hapmap]
rs13076508	1.00[JPT][hapmap];0.83[AMR][1000 genomes]
rs13076890	1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs13089892	0.82[MEX][hapmap];0.92[TSI][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13091360	1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13091545	1.00[JPT][hapmap]
rs13096571	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13098856	0.83[AMR][1000 genomes]
rs1541495	0.82[CEU][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.86[TSI][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs164637	1.00[JPT][hapmap];0.82[MEX][hapmap];0.92[TSI][hapmap]
rs17052058	1.00[JPT][hapmap]
rs17052061	1.00[JPT][hapmap]
rs17052068	1.00[JPT][hapmap]
rs2016575	0.85[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs2109557	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2109558	0.82[CEU][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2109559	0.82[CEU][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2159607	1.00[JPT][hapmap]
rs2215466	1.00[JPT][hapmap];0.92[TSI][hapmap];0.83[EUR][1000 genomes]
rs2335640	1.00[JPT][hapmap]
rs2335929	0.81[EUR][1000 genomes]
rs28481563	0.92[ASN][1000 genomes]
rs2878549	1.00[JPT][hapmap];0.82[MEX][hapmap];0.85[TSI][hapmap];0.93[EUR][1000 genomes]
rs34181173	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs34332947	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs34551211	1.00[JPT][hapmap];0.82[MEX][hapmap];0.92[TSI][hapmap]
rs34628357	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs34762015	1.00[JPT][hapmap]
rs34827613	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs35130772	0.83[AMR][1000 genomes]
rs352142	1.00[JPT][hapmap]
rs352143	1.00[JPT][hapmap]
rs352144	1.00[JPT][hapmap]
rs353548	1.00[JPT][hapmap];0.85[TSI][hapmap]
rs35860312	1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs35982798	0.81[EUR][1000 genomes]
rs3755810	0.92[TSI][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3774409	1.00[JPT][hapmap];0.82[MEX][hapmap];0.85[TSI][hapmap];0.81[EUR][1000 genomes]
rs3774410	1.00[JPT][hapmap]
rs3796342	0.83[AMR][1000 genomes]
rs3796343	1.00[JPT][hapmap]
rs390802	0.85[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs419050	1.00[JPT][hapmap];0.82[MEX][hapmap];0.92[TSI][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs419604	1.00[JPT][hapmap];0.82[MEX][hapmap];0.92[TSI][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs419752	1.00[JPT][hapmap];0.92[TSI][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4312651	1.00[JPT][hapmap];0.82[MEX][hapmap];0.85[TSI][hapmap];0.81[EUR][1000 genomes]
rs4687541	0.81[EUR][1000 genomes]
rs4687543	0.81[EUR][1000 genomes]
rs4687544	0.81[EUR][1000 genomes]
rs4687614	1.00[JPT][hapmap]
rs4687617	0.82[CEU][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4687618	1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs4687619	1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs4687621	0.81[EUR][1000 genomes]
rs498778	1.00[JPT][hapmap];0.82[MEX][hapmap];0.85[TSI][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs498946	0.85[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs575476	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs613519	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.85[TSI][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61734640	0.81[EUR][1000 genomes]
rs634382	0.85[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs6414568	0.81[EUR][1000 genomes]
rs6445386	1.00[JPT][hapmap]
rs6445484	0.81[EUR][1000 genomes]
rs6445485	0.81[EUR][1000 genomes]
rs6445486	1.00[JPT][hapmap];0.82[MEX][hapmap];0.85[TSI][hapmap];0.81[EUR][1000 genomes]
rs6445506	0.82[CEU][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.88[EUR][1000 genomes]
rs66462821	0.92[ASN][1000 genomes]
rs676034	1.00[JPT][hapmap];0.92[TSI][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6763882	1.00[JPT][hapmap]
rs6771558	1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs6782162	0.81[EUR][1000 genomes]
rs6784615	0.82[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6787493	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6795333	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6796333	1.00[JPT][hapmap]
rs6800707	1.00[JPT][hapmap]
rs6810027	1.00[JPT][hapmap];0.82[MEX][hapmap];0.85[TSI][hapmap];0.81[EUR][1000 genomes]
rs71297391	0.81[EUR][1000 genomes]
rs71297394	0.81[EUR][1000 genomes]
rs71297395	0.81[EUR][1000 genomes]
rs71297396	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs728408	0.82[CEU][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs758800	0.85[TSI][hapmap];0.81[EUR][1000 genomes]
rs758803	1.00[JPT][hapmap];0.82[MEX][hapmap];0.85[TSI][hapmap];0.81[EUR][1000 genomes]
rs7620015	0.82[CEU][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs82825	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs887514	0.82[CEU][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs887515	1.00[JPT][hapmap]
rs929528	1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs9844183	1.00[JPT][hapmap]
rs9846089	1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs9847332	0.81[EUR][1000 genomes]
rs9850471	0.81[EUR][1000 genomes]
rs9855470	1.00[JPT][hapmap];0.82[MEX][hapmap];0.85[TSI][hapmap];0.81[EUR][1000 genomes]
rs9861879	0.85[ASN][1000 genomes]
rs9863753	0.82[CEU][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9867823	1.00[JPT][hapmap];0.82[MEX][hapmap];0.85[TSI][hapmap];0.81[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	nsv876789	chr3:52247110-52575831	Flanking Active TSS Bivalent Enhancer Strong transcription Weak transcription Enhancers Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	117 gene(s)	inside rSNPs	diseases
2	nsv984542	chr3:52285682-52516115	Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	94 gene(s)	inside rSNPs	diseases
3	nsv834696	chr3:52317478-52479537	Flanking Active TSS Active TSS Strong transcription Weak transcription Bivalent Enhancer Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	45 gene(s)	inside rSNPs	diseases
4	nsv834697	chr3:52400578-52579417	Weak transcription Active TSS Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
5	nsv876792	chr3:52430526-52575831	Flanking Active TSS Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
6	esv3325653	chr3:52442937-52445885	Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
7	esv3354699	chr3:52443212-52445760	Flanking Active TSS Active TSS Weak transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	19 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	chr3:52438000-52443400	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr3:52441800-52443600	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr3:52442400-52443400	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr3:52442400-52443400	Genic enhancers	Lung	lung
5	chr3:52442400-52443800	Transcr. at gene 5' and 3'	Dnd41	blood
6	chr3:52442400-52445200	Active TSS	iPS-18 Cell Line	embryonic stem cell
7	chr3:52442600-52443400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr3:52442600-52443600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr3:52442600-52443600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
10	chr3:52442600-52443600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr3:52442600-52443600	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr3:52442600-52443600	Flanking Active TSS	Brain Hippocampus Middle	brain
13	chr3:52442600-52443600	Flanking Active TSS	Colonic Mucosa	Colon
14	chr3:52442600-52443600	Flanking Active TSS	Colon Smooth Muscle	Colon
15	chr3:52442600-52443600	Flanking Active TSS	Hela-S3	cervix
16	chr3:52442600-52443800	Flanking Active TSS	Fetal Brain Male	brain
17	chr3:52442600-52443800	Transcr. at gene 5' and 3'	Skeletal Muscle Male	skeletal muscle
18	chr3:52442600-52445800	Active TSS	H9 Cell Line	embryonic stem cell
19	chr3:52442800-52443400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr3:52442800-52443400	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
21	chr3:52442800-52443400	Flanking Active TSS	GM12878-XiMat	blood
22	chr3:52442800-52443400	Flanking Active TSS	HepG2	liver
23	chr3:52442800-52443400	Flanking Active TSS	NHDF-Ad	bronchial
24	chr3:52442800-52443400	Flanking Active TSS	NHLF	lung
25	chr3:52442800-52443600	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr3:52442800-52443600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
27	chr3:52442800-52443600	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
28	chr3:52442800-52443600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
29	chr3:52442800-52443600	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr3:52442800-52443600	Flanking Active TSS	Brain Anterior Caudate	brain
31	chr3:52442800-52443600	Flanking Active TSS	Left Ventricle	heart
32	chr3:52442800-52443600	Flanking Active TSS	Rectal Smooth Muscle	rectum
33	chr3:52442800-52443600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
34	chr3:52442800-52443600	Flanking Active TSS	HSMMtube	muscle
35	chr3:52442800-52443600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
36	chr3:52442800-52443600	Flanking Active TSS	NH-A	brain
37	chr3:52442800-52443800	Flanking Active TSS	Primary hematopoietic stem cells	blood
38	chr3:52442800-52443800	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
39	chr3:52442800-52443800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr3:52442800-52443800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr3:52442800-52443800	Flanking Active TSS	Duodenum Mucosa	Duodenum
42	chr3:52442800-52443800	Transcr. at gene 5' and 3'	Fetal Intestine Small	intestine
43	chr3:52442800-52445200	Active TSS	HUES64 Cell Line	embryonic stem cell
44	chr3:52442800-52446400	Active TSS	HUES6 Cell Line	embryonic stem cell
45	chr3:52443000-52443400	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr3:52443000-52443400	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr3:52443000-52443400	Flanking Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr3:52443000-52443400	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
49	chr3:52443000-52443400	Transcr. at gene 5' and 3'	iPS-20b Cell Line	embryonic stem cell
50	chr3:52443000-52443400	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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