Variant report

Variant	rs3794098
Chromosome Location	chr11:35298608-35298609
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:11)
CpG islands
(count:0)
Chromatin interactive
region (count:16)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:11 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MYC	chr11:35297864-35298627	MCF10A-Er-Src	breast:	n/a	n/a
2	FOS	chr11:35297867-35298618	MCF10A-Er-Src	breast:	n/a	chr11:35298189-35298199 chr11:35298189-35298199
3	POLR2A	chr11:35296637-35299041	MCF10A-Er-Src	breast:	n/a	n/a
4	STAT3	chr11:35297917-35298658	MCF10A-Er-Src	breast:	n/a	n/a
5	CEBPB	chr11:35298020-35298638	Hela-S3	cervix:	n/a	n/a
6	POLR2A	chr11:35298574-35299665	HepG2	liver:	n/a	n/a
7	FOS	chr11:35297853-35298708	MCF10A-Er-Src	breast:	n/a	chr11:35298189-35298199 chr11:35298189-35298199
8	STAT3	chr11:35297862-35298689	MCF10A-Er-Src	breast:	n/a	n/a
9	FOS	chr11:35297842-35298674	MCF10A-Er-Src	breast:	n/a	chr11:35298189-35298199 chr11:35298189-35298199
10	STAT3	chr11:35297867-35298658	MCF10A-Er-Src	breast:	n/a	n/a
11	MYC	chr11:35297874-35298658	MCF10A-Er-Src	breast:	n/a	n/a

No data

(count:16 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:35295544..35300568-chr11:35411012..35415613,12	MCF-7	breast:
2	chr11:35296393..35299239-chr11:35321484..35323534,3	MCF-7	breast:
3	chr11:35295515..35301483-chr11:35383053..35389477,19	MCF-7	breast:
4	chr11:35297080..35299545-chr11:35312550..35314552,2	MCF-7	breast:
5	chr11:35298068..35300240-chr11:35306862..35309104,3	MCF-7	breast:
6	chr11:35296687..35299158-chr11:35300780..35302460,2	K562	blood:
7	chr11:35295688..35300934-chr11:35309144..35319083,18	MCF-7	breast:
8	chr11:35289687..35293483-chr11:35296744..35298908,3	MCF-7	breast:
9	chr11:35296358..35301253-chr11:35383072..35388147,10	MCF-7	breast:
10	chr11:18548166..18548951-chr11:35297909..35298657,2	Hela-S3	cervix:
11	chr11:35295425..35298898-chr11:35346407..35348803,4	MCF-7	breast:
12	chr11:35296515..35299652-chr11:35423102..35425675,4	MCF-7	breast:
13	chr11:35295369..35301669-chr11:35315160..35319353,7	MCF-7	breast:
14	chr11:35279012..35286392-chr11:35294737..35300890,10	MCF-7	breast:
15	chr11:35296537..35299593-chr11:35342637..35345511,4	MCF-7	breast:
16	chr11:35294659..35299259-chr11:35323739..35329418,10	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000255004	TF binding region
ENSG00000074319	Chromatin interaction
ENSG00000110436	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs1043101	1.00[CEU][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10742339	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10742340	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10742341	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10768118	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10768120	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10768121	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10768122	1.00[CEU][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10768123	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10768126	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10836360	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10836361	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10836362	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10836363	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10836364	1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10836367	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10836369	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11033045	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11033046	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11033048	1.00[CEU][hapmap];0.83[CHD][hapmap];0.98[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11524863	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12361171	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12796856	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1570214	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1570215	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17378105	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3088168	1.00[CEU][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs35629461	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3763888	1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3794086	0.92[CEU][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3794089	0.96[CEU][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3794090	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3794091	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3794099	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3794100	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3794101	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3794102	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3794103	1.00[CEU][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3847604	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4755394	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4755395	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4756203	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4756204	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4756205	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4756206	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57339940	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6484778	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7105505	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7105690	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7121587	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs736374	0.83[EUR][1000 genomes]
rs7946149	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs932633	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs932635	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs957350	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9633870	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1045837	chr11:34893992-35395190	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
2	nsv832120	chr11:35277410-35490304	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:35265800-35305800	Weak transcription	HepG2	liver
2	chr11:35270400-35307000	Weak transcription	Fetal Brain Male	brain
3	chr11:35283000-35302000	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr11:35284600-35300800	Weak transcription	Brain Angular Gyrus	brain
5	chr11:35285800-35308800	Weak transcription	Gastric	stomach
6	chr11:35295000-35298800	Weak transcription	Esophagus	oesophagus
7	chr11:35295400-35298800	Weak transcription	Primary T helper cells PMA-I stimulated	--
8	chr11:35296000-35298800	Enhancers	Stomach Mucosa	stomach
9	chr11:35296000-35299000	Enhancers	HMEC	breast
10	chr11:35296000-35299000	Enhancers	NHEK	skin
11	chr11:35296400-35299000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
12	chr11:35296600-35298800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr11:35296600-35298800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr11:35296600-35298800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr11:35296600-35298800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr11:35296600-35299000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr11:35296600-35301200	Enhancers	Pancreas	Pancrea
18	chr11:35296800-35300400	Weak transcription	Fetal Brain Female	brain
19	chr11:35297000-35299000	Enhancers	Fetal Thymus	thymus
20	chr11:35297200-35299200	Weak transcription	Duodenum Mucosa	Duodenum
21	chr11:35297200-35302200	Weak transcription	Skeletal Muscle Female	skeletal muscle
22	chr11:35297400-35298800	Enhancers	Stomach Smooth Muscle	stomach
23	chr11:35297400-35302200	Weak transcription	Adipose Nuclei	Adipose
24	chr11:35297600-35298800	Weak transcription	Brain Cingulate Gyrus	brain
25	chr11:35297600-35299200	Weak transcription	Liver	Liver
26	chr11:35297600-35302200	Weak transcription	Fetal Stomach	stomach
27	chr11:35297600-35302200	Weak transcription	Left Ventricle	heart
28	chr11:35297600-35302200	Weak transcription	Right Atrium	heart
29	chr11:35297600-35302600	Weak transcription	Muscle Satellite Cultured Cells	--
30	chr11:35297600-35303000	Weak transcription	HSMMtube	muscle
31	chr11:35297600-35303400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr11:35297800-35300800	Weak transcription	Brain Germinal Matrix	brain
33	chr11:35297800-35303200	Weak transcription	Rectal Smooth Muscle	rectum
34	chr11:35298000-35299000	Enhancers	Hela-S3	cervix
35	chr11:35298000-35317200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
36	chr11:35298200-35298800	Enhancers	Brain Anterior Caudate	brain
37	chr11:35298200-35302400	Weak transcription	Aorta	Aorta
38	chr11:35298200-35303600	Weak transcription	A549	lung
39	chr11:35298200-35303800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr11:35298200-35326000	Weak transcription	Brain Substantia Nigra	brain
41	chr11:35298400-35301200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr11:35298400-35302200	Weak transcription	NHDF-Ad	bronchial
43	chr11:35298400-35302200	Weak transcription	NHLF	lung
44	chr11:35298400-35302600	Weak transcription	Thymus	Thymus
45	chr11:35298400-35303600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr11:35298400-35303600	Weak transcription	Osteobl	bone
47	chr11:35298600-35298800	Enhancers	Brain Hippocampus Middle	brain
48	chr11:35298600-35298800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
49	chr11:35298600-35299600	Genic enhancers	Cortex derived primary cultured neurospheres	brain
50	chr11:35298600-35302000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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