Variant report

Variant	rs9836915
Chromosome Location	chr3:98625303-98625304
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	CBX3	chr3:98624962-98625582	HCT-116	colon:	n/a	n/a
2	TEAD4	chr3:98624988-98625546	HCT-116	colon:	n/a	n/a
3	SP1	chr3:98624817-98625655	HCT-116	colon:	n/a	n/a
4	YY1	chr3:98625139-98625375	HCT-116	colon:	n/a	n/a
5	MAX	chr3:98624922-98625563	A549	lung:	n/a	n/a
6	STAT3	chr3:98625172-98625409	MCF10A-Er-Src	breast:	n/a	chr3:98625235-98625244 chr3:98625236-98625245
7	NFIC	chr3:98624960-98625533	ECC-1	luminal epithelium:	n/a	n/a
8	FOXM1	chr3:98624874-98625497	SK-N-SH	brain:	n/a	n/a
9	YY1	chr3:98625083-98625351	SK-N-SH_RA	brain:	n/a	n/a
10	TCF7L2	chr3:98625057-98625480	Hela-S3	cervix:	n/a	chr3:98625376-98625392 chr3:98625376-98625392 chr3:98625377-98625391 chr3:98625379-98625388
11	JUND	chr3:98624929-98625523	SK-N-SH	brain:	n/a	chr3:98625032-98625041
12	RXRA	chr3:98624974-98625573	SK-N-SH	brain:	n/a	n/a
13	EP300	chr3:98624816-98625625	SK-N-SH	brain:	n/a	n/a
14	NFIC	chr3:98624951-98625583	SK-N-SH	brain:	n/a	n/a
15	SP1	chr3:98624823-98625650	A549	lung:	n/a	n/a
16	TCF12	chr3:98624758-98625722	A549	lung:	n/a	n/a
17	NFIC	chr3:98624820-98625566	ECC-1	luminal epithelium:	n/a	n/a
18	TCF7L2	chr3:98625094-98625576	HCT-116	colon:	n/a	chr3:98625376-98625392 chr3:98625376-98625392 chr3:98625377-98625391 chr3:98625379-98625388
19	TEAD4	chr3:98624920-98625543	ECC-1	luminal epithelium:	n/a	n/a
20	PBX3	chr3:98624920-98625629	SK-N-SH	brain:	n/a	n/a
21	EP300	chr3:98624908-98625700	A549	lung:	n/a	n/a
22	TCF12	chr3:98624907-98625672	SK-N-SH	brain:	n/a	n/a
23	NR3C1	chr3:98625172-98625548	A549	lung:	n/a	n/a
24	FOXA1	chr3:98625073-98625577	A549	lung:	n/a	chr3:98625262-98625274
25	TAF1	chr3:98625168-98625491	SK-N-SH	brain:	n/a	n/a
26	GATA3	chr3:98624983-98625544	A549	lung:	n/a	n/a
27	FOXM1	chr3:98624906-98625603	ECC-1	luminal epithelium:	n/a	n/a
28	FOS	chr3:98625069-98625444	MCF10A-Er-Src	breast:	n/a	n/a
29	FOS	chr3:98625096-98625399	MCF10A-Er-Src	breast:	n/a	n/a
30	NFIC	chr3:98624827-98625632	SK-N-SH	brain:	n/a	n/a
31	NR3C1	chr3:98625078-98625535	A549	lung:	n/a	n/a
32	REST	chr3:98624959-98625671	A549	lung:	n/a	n/a
33	POLR2A	chr3:98624917-98625563	U87	brain:	n/a	n/a
34	POLR2A	chr3:98624998-98625527	HCT-116	colon:	n/a	n/a
35	SP1	chr3:98624923-98625653	A549	lung:	n/a	n/a
36	FOS	chr3:98625055-98625436	MCF10A-Er-Src	breast:	n/a	n/a
37	POLR2A	chr3:98624945-98625557	U87	brain:	n/a	n/a
38	NR3C1	chr3:98625048-98625575	A549	lung:	n/a	n/a
39	RXRA	chr3:98624965-98625577	SK-N-SH	brain:	n/a	n/a
40	FOS	chr3:98625109-98625462	HUVEC	blood vessel:	n/a	n/a
41	YY1	chr3:98624999-98625434	SK-N-SH	brain:	n/a	n/a
42	TCF12	chr3:98624817-98625712	SK-N-SH	brain:	n/a	n/a
43	POLR2A	chr3:98624945-98625532	SK-N-SH	brain:	n/a	n/a
44	FOSL2	chr3:98624829-98625651	SK-N-SH	brain:	n/a	chr3:98625032-98625041
45	NR3C1	chr3:98625020-98625579	A549	lung:	n/a	n/a
46	FOSL1	chr3:98624938-98625689	HCT-116	colon:	n/a	chr3:98625032-98625041
47	FOSL2	chr3:98625063-98625470	A549	lung:	n/a	n/a
48	FOXA1	chr3:98625093-98625590	A549	lung:	n/a	chr3:98625262-98625274
49	JUND	chr3:98624908-98625638	SK-N-SH	brain:	n/a	chr3:98625032-98625041
50	JUND	chr3:98625041-98625579	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:98620185..98622258-chr3:98623304..98625603,3	MCF-7	breast:
2	chr3:98609933..98612061-chr3:98623742..98626335,2	K562	blood:
3	chr3:98619082..98623514-chr3:98623819..98627236,6	K562	blood:

Variant related genes	Relation type
RNU6-1263P	TF binding region
DCBLD2	TF binding region
ENSG00000239462	Chromatin interaction
ENSG00000057019	Chromatin interaction

Extended variants
information (count: 64 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs10084679	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs12330381	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13317610	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13318960	0.83[AMR][1000 genomes]
rs13320266	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13320890	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13322253	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13327449	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13327485	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs28417568	0.88[ASN][1000 genomes]
rs28429424	0.83[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs28489284	0.88[ASN][1000 genomes]
rs28528154	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs28650813	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs28821579	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs28883308	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs28890260	0.83[AMR][1000 genomes]
rs3796133	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[ASN][1000 genomes]
rs56172805	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56857413	0.94[ASN][1000 genomes]
rs57962467	0.94[ASN][1000 genomes]
rs59906228	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72932691	0.82[ASN][1000 genomes]
rs72932700	0.83[ASN][1000 genomes]
rs72934623	0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs72934641	0.83[ASN][1000 genomes]
rs72938540	0.86[EUR][1000 genomes]
rs72938577	0.94[ASN][1000 genomes]
rs9289696	0.86[EUR][1000 genomes]
rs9289699	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9289700	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9810407	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9812438	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[ASN][1000 genomes]
rs9818215	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9819279	0.86[EUR][1000 genomes]
rs9819309	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9828045	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9833945	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9836437	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9838166	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9838238	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9838706	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[ASN][1000 genomes]
rs9839559	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9842226	0.86[EUR][1000 genomes]
rs9842555	0.83[AMR][1000 genomes]
rs9848335	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9848583	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9850469	0.86[EUR][1000 genomes]
rs9852537	1.00[AMR][1000 genomes]
rs9852889	0.86[EUR][1000 genomes]
rs9859042	0.86[EUR][1000 genomes]
rs9862660	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[ASN][1000 genomes]
rs9864010	0.86[EUR][1000 genomes]
rs9870500	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs9870940	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9872073	0.85[EUR][1000 genomes]
rs9872301	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9879302	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9883751	1.00[EUR][1000 genomes];1.00[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	nsv591065	chr3:98204198-98766326	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv1007140	chr3:98421229-99202458	Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
3	nsv536663	chr3:98421229-99202458	Enhancers ZNF genes & repeats Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
4	nsv877214	chr3:98445324-98738006	Enhancers Genic enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
5	nsv1007486	chr3:98597738-99249081	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:98621600-98625400	Weak transcription	Psoas Muscle	Psoas
2	chr3:98623000-98628000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr3:98623600-98636400	Weak transcription	Fetal Heart	heart
4	chr3:98624800-98625600	Enhancers	HUVEC	blood vessel
5	chr3:98624800-98626600	Enhancers	NHLF	lung
6	chr3:98625000-98625400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr3:98625000-98625400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr3:98625000-98625400	Enhancers	Fetal Lung	lung
9	chr3:98625000-98625600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr3:98625000-98625600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr3:98625000-98625600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr3:98625000-98625600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr3:98625000-98625600	Enhancers	Cortex derived primary cultured neurospheres	brain
14	chr3:98625000-98625600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr3:98625000-98625600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr3:98625000-98625600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr3:98625000-98625600	Enhancers	Hela-S3	cervix
18	chr3:98625000-98625600	Enhancers	HMEC	breast
19	chr3:98625000-98625600	Enhancers	HSMMtube	muscle
20	chr3:98625000-98625800	Flanking Active TSS	A549	lung
21	chr3:98625000-98626000	Flanking Active TSS	NH-A	brain
22	chr3:98625000-98626000	Enhancers	NHEK	skin
23	chr3:98625000-98626200	Enhancers	HSMM	muscle
24	chr3:98625000-98626400	Enhancers	Osteobl	bone
25	chr3:98625200-98625400	ZNF genes & repeats	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr3:98625200-98625400	Enhancers	Muscle Satellite Cultured Cells	--
27	chr3:98625200-98625600	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr3:98625200-98625600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
29	chr3:98625200-98625600	Flanking Active TSS	NHDF-Ad	bronchial
30	chr3:98625200-98626400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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