Variant report

Variant	rs6963804
Chromosome Location	chr7:40171517-40171518
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	chr7:40168616-40174782	MCF10A-Er-Src	breast:	n/a	n/a
2	POLR2A	chr7:40171002-40172001	HepG2	liver:	n/a	n/a
3	CEBPB	chr7:40171420-40171625	A549	lung:	n/a	chr7:40171563-40171574
4	POLR2A	chr7:40171206-40171617	K562	blood:	n/a	n/a
5	POLR2A	chr7:40170533-40171543	Hela-S3	cervix:	n/a	n/a
6	POLR2A	chr7:40168497-40173052	K562	blood:	n/a	n/a
7	CEBPB	chr7:40171368-40171731	HepG2	liver:	n/a	chr7:40171563-40171574

No.	Distal block	Cell Line	Cell type
1	chr7:40167264..40171884-chr7:40172209..40175327,5	K562	blood:
2	chr7:39922523..39924083-chr7:40170762..40172465,2	K562	blood:
3	chr20:45945819..45948556-chr7:40171300..40173134,2	MCF-7	breast:
4	chr7:39957754..39959391-chr7:40170682..40173574,2	MCF-7	breast:
5	chr7:40162725..40164570-chr7:40170579..40173215,2	MCF-7	breast:

Variant related genes	Relation type
SUGCT	TF binding region
ENSG00000199273	TF binding region
ENSG00000267882	Chromatin interaction
ENSG00000175600	Chromatin interaction
ENSG00000168303	Chromatin interaction
ENSG00000101040	Chromatin interaction

Extended variants
information (count: 141 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:128)

rs_ID	r²[population]
rs10081308	0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10081355	0.92[ASN][1000 genomes]
rs10156182	0.90[EUR][1000 genomes]
rs10227386	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10228020	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10229517	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10230530	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10234693	0.91[EUR][1000 genomes]
rs10242519	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10243494	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10246466	0.90[EUR][1000 genomes]
rs1024680	0.91[EUR][1000 genomes]
rs10259565	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10261251	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10267954	0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10268288	0.92[EUR][1000 genomes]
rs10269349	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10272641	0.89[EUR][1000 genomes]
rs10275761	0.89[EUR][1000 genomes]
rs10276687	0.88[ASN][1000 genomes]
rs1082028	0.88[EUR][1000 genomes]
rs1082030	0.81[EUR][1000 genomes]
rs10951626	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10951627	0.88[ASN][1000 genomes]
rs11760739	0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11763047	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11767697	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11768838	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11769327	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11980745	0.89[EUR][1000 genomes]
rs12333691	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12333929	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12334141	0.86[EUR][1000 genomes]
rs12530776	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12533272	0.88[EUR][1000 genomes]
rs12534074	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12535524	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1257699	0.88[EUR][1000 genomes]
rs13231777	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13233333	0.96[ASN][1000 genomes]
rs1403381	0.89[EUR][1000 genomes]
rs1406565	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1406566	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1534675	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1568645	0.94[EUR][1000 genomes]
rs1830422	0.86[ASN][1000 genomes]
rs1874232	0.94[ASN][1000 genomes]
rs1874233	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1881683	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1881684	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1919615	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1973398	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1989589	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2009560	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2019838	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2024200	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2036041	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2052097	0.91[EUR][1000 genomes]
rs2056775	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2109340	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2159488	0.90[EUR][1000 genomes]
rs2329693	0.91[EUR][1000 genomes]
rs2329695	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28733232	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28742222	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs33999222	0.89[EUR][1000 genomes]
rs34960564	0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs3847020	0.92[EUR][1000 genomes]
rs3847021	0.93[EUR][1000 genomes]
rs388354	0.89[ASN][1000 genomes]
rs3966459	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4720354	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4723929	0.93[EUR][1000 genomes]
rs4723931	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4723934	0.88[ASN][1000 genomes]
rs6462961	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6462963	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6462965	0.87[ASN][1000 genomes]
rs66481381	0.88[ASN][1000 genomes]
rs66912039	0.86[ASN][1000 genomes]
rs67438499	0.88[ASN][1000 genomes]
rs6944166	0.88[ASN][1000 genomes]
rs6948982	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6951375	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6952597	0.90[EUR][1000 genomes]
rs6954096	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6957274	0.90[ASN][1000 genomes]
rs6957766	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6960111	0.91[EUR][1000 genomes]
rs6962410	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6966917	0.89[EUR][1000 genomes]
rs6968402	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6975853	0.93[EUR][1000 genomes]
rs6978474	0.80[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs6979628	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs71560176	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs731847	0.89[EUR][1000 genomes]
rs731848	0.89[EUR][1000 genomes]
rs773379	0.82[EUR][1000 genomes]
rs773381	0.83[EUR][1000 genomes]
rs773385	0.88[EUR][1000 genomes]
rs773386	0.88[EUR][1000 genomes]
rs773393	0.87[EUR][1000 genomes]
rs773397	0.87[EUR][1000 genomes]
rs773402	0.88[EUR][1000 genomes]
rs773403	0.88[EUR][1000 genomes]
rs773413	0.89[EUR][1000 genomes]
rs773414	0.88[EUR][1000 genomes]
rs773415	0.81[EUR][1000 genomes]
rs773424	0.88[EUR][1000 genomes]
rs7776964	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7776967	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7778061	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7779560	0.82[ASN][1000 genomes]
rs7780858	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7796371	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7797041	0.89[EUR][1000 genomes]
rs7799846	0.88[EUR][1000 genomes]
rs7802584	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7808529	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7809368	0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7810509	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs887445	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs887447	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9639818	0.91[EUR][1000 genomes]
rs9639824	0.86[ASN][1000 genomes]
rs9690188	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9791485	0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2756801	chr7:40060180-40269583	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
2	esv2759525	chr7:40060180-40269583	Strong transcription Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
3	nsv887979	chr7:40067021-40193535	Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
4	nsv887980	chr7:40067021-40203356	Strong transcription Genic enhancers Weak transcription Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
5	nsv887981	chr7:40075461-40203356	Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
6	nsv971193	chr7:40075881-40197955	Strong transcription Enhancers Weak transcription Bivalent/Poised TSS Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
7	esv34547	chr7:40077032-40230965	Strong transcription Enhancers Active TSS ZNF genes & repeats Weak transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
8	nsv824080	chr7:40077089-40198644	Weak transcription Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
9	nsv464437	chr7:40094641-40197168	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
10	nsv606709	chr7:40094641-40197168	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
11	nsv1032278	chr7:40097371-40396300	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
12	nsv887982	chr7:40098787-40193535	Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats 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 miRNA target site	16 gene(s)	inside rSNPs	diseases
13	nsv1024735	chr7:40149227-40203356	Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:40134600-40171800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr7:40134600-40173200	Weak transcription	Lung	lung
3	chr7:40135000-40172800	Weak transcription	Fetal Kidney	kidney
4	chr7:40135600-40173000	Weak transcription	Fetal Muscle Leg	muscle
5	chr7:40136000-40172200	Weak transcription	Osteobl	bone
6	chr7:40136200-40171800	Weak transcription	Muscle Satellite Cultured Cells	--
7	chr7:40136600-40173200	Weak transcription	Placenta	Placenta
8	chr7:40137400-40172000	Weak transcription	Fetal Lung	lung
9	chr7:40137600-40171800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr7:40137600-40172200	Weak transcription	A549	lung
11	chr7:40137800-40171800	Weak transcription	Colon Smooth Muscle	Colon
12	chr7:40152400-40171800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr7:40152600-40171600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr7:40152600-40171600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr7:40152600-40172800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr7:40157400-40171600	Weak transcription	NH-A	brain
17	chr7:40157400-40171800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
18	chr7:40157400-40171800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr7:40157400-40172600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr7:40157400-40172600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr7:40158400-40171800	Weak transcription	Thymus	Thymus
22	chr7:40160200-40171600	Weak transcription	Fetal Heart	heart
23	chr7:40160200-40172000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
24	chr7:40160200-40172200	Weak transcription	HUES6 Cell Line	embryonic stem cell
25	chr7:40161600-40172600	Weak transcription	Primary hematopoietic stem cells	blood
26	chr7:40161600-40172600	Weak transcription	Aorta	Aorta
27	chr7:40162000-40172600	Weak transcription	Rectal Mucosa Donor 29	rectum
28	chr7:40162800-40171800	Weak transcription	Duodenum Mucosa	Duodenum
29	chr7:40163000-40173200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr7:40164400-40172000	Weak transcription	NHEK	skin
31	chr7:40164600-40172600	Weak transcription	Monocytes-CD14+_RO01746	blood
32	chr7:40164800-40172600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr7:40165400-40172800	Weak transcription	H1 Cell Line	embryonic stem cell
34	chr7:40165600-40172000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
35	chr7:40165800-40173400	Weak transcription	Placenta Amnion	Placenta Amnion
36	chr7:40166200-40172400	Weak transcription	HUES48 Cell Line	embryonic stem cell
37	chr7:40166600-40172600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
38	chr7:40166800-40172200	Weak transcription	Rectal Mucosa Donor 31	rectum
39	chr7:40167000-40171800	Weak transcription	HUVEC	blood vessel
40	chr7:40167400-40172600	Weak transcription	Fetal Intestine Large	intestine
41	chr7:40167600-40171800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr7:40167600-40172600	Weak transcription	Fetal Stomach	stomach
43	chr7:40167800-40172200	Weak transcription	HMEC	breast
44	chr7:40167800-40173000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
45	chr7:40167800-40173000	Weak transcription	Fetal Thymus	thymus
46	chr7:40167800-40173200	Weak transcription	Fetal Muscle Trunk	muscle
47	chr7:40168000-40172600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
48	chr7:40168600-40172400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
49	chr7:40168800-40171600	Weak transcription	Primary B cells from cord blood	blood
50	chr7:40168800-40171800	Weak transcription	Skeletal Muscle Female	skeletal muscle

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