Variant report

Variant	rs3962133
Chromosome Location	chr7:66207246-66207247
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:6)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:6 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr7:66207222-66207685	SK-N-SH	brain:	n/a	n/a
2	FOSL2	chr7:66207238-66207773	HepG2	liver:	n/a	n/a
3	CHD1	chr7:66207241-66207699	IMR90	lung:	n/a	n/a
4	POLR2A	chr7:66207224-66207527	GM12878	blood:	n/a	n/a
5	POLR2A	chr7:66207201-66207670	Hela-S3	cervix:	n/a	n/a
6	POLR2A	chr7:66207238-66207910	GM12878	blood:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr7:66117717..66119604-chr7:66204829..66207389,2	K562	blood:
2	chr7:66204928..66209821-chr7:66213597..66216412,7	MCF-7	breast:
3	chr7:66205946..66208187-chr7:66309676..66311325,2	MCF-7	breast:
4	chr7:66205725..66207353-chr7:66207678..66209182,2	MCF-7	breast:
5	chr7:66144687..66148625-chr7:66203954..66207507,6	K562	blood:
6	chr7:66144717..66148625-chr7:66203954..66207507,5	K562	blood:
7	chr7:66203955..66208659-chr7:66209716..66215353,8	K562	blood:
8	chr7:66118548..66121026-chr7:66205734..66207315,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000272831	TF binding region
ENSG00000154710	Chromatin interaction
ENSG00000271064	Chromatin interaction
ENSG00000226824	Chromatin interaction
ENSG00000230583	Chromatin interaction

Extended variants
information (count: 126 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:121)

rs_ID	r²[population]
rs10081172	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10156059	0.83[AFR][1000 genomes]
rs10224189	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10224536	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10225392	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10226191	0.90[AFR][1000 genomes];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10226294	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10228381	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10229580	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10231860	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10234640	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10234747	0.84[EUR][1000 genomes]
rs10235037	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10236665	0.81[ASN][1000 genomes]
rs10239200	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10240153	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10240582	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10241395	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10242870	0.81[AFR][1000 genomes]
rs10243608	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10244459	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10244602	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10245017	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10247324	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10247815	0.83[AFR][1000 genomes];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10247852	0.85[ASN][1000 genomes]
rs10255813	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10256117	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10258628	0.84[EUR][1000 genomes]
rs10264619	0.84[ASN][1000 genomes]
rs10265069	0.80[AFR][1000 genomes]
rs10265154	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10266041	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10266792	0.82[EUR][1000 genomes]
rs10267834	0.83[EUR][1000 genomes]
rs10270326	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10271177	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10273320	0.84[EUR][1000 genomes]
rs10273402	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10277231	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10278343	0.84[EUR][1000 genomes]
rs10278763	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10280717	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10281544	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10282310	0.84[EUR][1000 genomes]
rs10282522	0.91[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs10479728	0.84[EUR][1000 genomes]
rs1060527	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1064795	0.84[EUR][1000 genomes]
rs12234826	0.84[EUR][1000 genomes]
rs12333749	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12334214	0.80[EUR][1000 genomes]
rs13437994	0.82[EUR][1000 genomes]
rs13438432	0.84[EUR][1000 genomes]
rs16868546	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17138274	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17747927	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17748115	0.82[EUR][1000 genomes]
rs1882656	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1882657	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1895134	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2013707	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28368585	0.84[EUR][1000 genomes]
rs28375318	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28379824	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28455065	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28460006	0.84[EUR][1000 genomes]
rs28474923	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28526115	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28533332	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28547918	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28560293	0.80[EUR][1000 genomes]
rs28606020	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28607736	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28634091	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28657758	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28663128	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3764904	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3778907	0.84[EUR][1000 genomes]
rs3778908	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3800814	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3814464	0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3823607	0.91[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs3823609	0.84[EUR][1000 genomes]
rs4587218	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs57774708	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs57875851	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs57902746	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs58973756	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs59079543	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs59693594	0.82[EUR][1000 genomes]
rs60026498	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61700307	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6964080	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6973897	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6974601	0.84[EUR][1000 genomes]
rs73133809	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73133816	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73133851	0.85[EUR][1000 genomes]
rs73133859	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73133865	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73135905	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73135907	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73135909	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73135917	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73135922	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73135925	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73135950	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73135960	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73135973	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73137960	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73137963	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73137978	0.86[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs73139941	0.88[EUR][1000 genomes]
rs73139976	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73141980	0.90[AFR][1000 genomes];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73145924	0.82[EUR][1000 genomes]
rs73152719	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7455757	0.81[AFR][1000 genomes]
rs7785883	0.81[AMR][1000 genomes]
rs9654843	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532124	chr7:65371521-66234730	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	125 gene(s)	inside rSNPs	diseases
2	nsv1026559	chr7:65617368-66370805	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	116 gene(s)	inside rSNPs	diseases
3	nsv888328	chr7:66173040-66327654	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
4	nsv971490	chr7:66192193-66212423	Genic enhancers Enhancers Flanking Bivalent TSS/Enh Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
5	nsv970871	chr7:66206610-66210233	Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3962133	GS1-124K5.12	cis	Skin Sun Exposed Lower leg	GTEx
rs3962133	GS1-124K5.12	cis	Artery Tibial	GTEx
rs3962133	GS1-124K5.12	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:66204200-66208000	Active TSS	HUES64 Cell Line	embryonic stem cell
2	chr7:66204400-66207400	Active TSS	Breast Myoepithelial Primary Cells	Breast
3	chr7:66204400-66207800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr7:66204600-66207400	Active TSS	HMEC	breast
5	chr7:66204600-66207600	Active TSS	NHDF-Ad	bronchial
6	chr7:66204600-66207800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr7:66204800-66207400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr7:66204800-66207600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr7:66204800-66207600	Active TSS	HSMMtube	muscle
10	chr7:66204800-66207600	Active TSS	NHLF	lung
11	chr7:66204800-66208000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr7:66205000-66207400	Active TSS	GM12878-XiMat	blood
13	chr7:66205000-66207400	Active TSS	Hela-S3	cervix
14	chr7:66205000-66207600	Active TSS	Muscle Satellite Cultured Cells	--
15	chr7:66205000-66207600	Active TSS	HSMM	muscle
16	chr7:66205200-66207400	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr7:66205200-66207400	Active TSS	NH-A	brain
18	chr7:66205200-66207800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr7:66205600-66207800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr7:66206200-66207600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
21	chr7:66206400-66207600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr7:66206400-66208000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr7:66206400-66216600	Weak transcription	Spleen	Spleen
24	chr7:66206600-66207400	Flanking Active TSS	Adipose Nuclei	Adipose
25	chr7:66206600-66207600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
26	chr7:66206600-66207600	Active TSS	HepG2	liver
27	chr7:66206600-66208000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
28	chr7:66206800-66207600	Enhancers	Brain Substantia Nigra	brain
29	chr7:66206800-66207600	Enhancers	Fetal Brain Male	brain
30	chr7:66206800-66207600	Enhancers	Gastric	stomach
31	chr7:66206800-66207600	Weak transcription	Placenta Amnion	Placenta Amnion
32	chr7:66206800-66207600	Enhancers	HUVEC	blood vessel
33	chr7:66206800-66208000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
34	chr7:66206800-66208000	Enhancers	Primary T helper cells fromperipheralblood	blood
35	chr7:66206800-66208000	Enhancers	Thymus	Thymus
36	chr7:66206800-66208200	Enhancers	Primary T cells fromperipheralblood	blood
37	chr7:66206800-66210600	Weak transcription	Fetal Heart	heart
38	chr7:66206800-66212800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
39	chr7:66206800-66213600	Weak transcription	Small Intestine	intestine
40	chr7:66206800-66216400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
41	chr7:66206800-66223400	Weak transcription	Sigmoid Colon	Sigmoid Colon
42	chr7:66206800-66232600	Weak transcription	Primary T cells from cord blood	blood
43	chr7:66206800-66238800	Weak transcription	Aorta	Aorta
44	chr7:66207000-66207400	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr7:66207000-66207400	Enhancers	Cortex derived primary cultured neurospheres	brain
46	chr7:66207000-66207400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr7:66207000-66207400	Weak transcription	Brain Angular Gyrus	brain
48	chr7:66207000-66207400	Weak transcription	Brain Cingulate Gyrus	brain
49	chr7:66207000-66207400	Enhancers	Brain Hippocampus Middle	brain
50	chr7:66207000-66207400	Enhancers	Placenta	Placenta

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