Variant report

Variant	rs11064631
Chromosome Location	chr12:1104827-1104828
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	FOS	chr12:1104689-1105271	MCF10A-Er-Src	breast:	n/a	n/a
2	FOS	chr12:1104662-1105286	MCF10A-Er-Src	breast:	n/a	n/a
3	E2F4	chr12:1104687-1105258	MCF10A-Er-Src	breast:	n/a	n/a
4	STAT3	chr12:1104610-1105282	MCF10A-Er-Src	breast:	n/a	chr12:1105078-1105089
5	STAT3	chr12:1104561-1105256	MCF10A-Er-Src	breast:	n/a	chr12:1105078-1105089
6	NFYB	chr12:1104804-1104883	Hela-S3	cervix:	n/a	n/a
7	STAT3	chr12:1104616-1105090	MCF10A-Er-Src	breast:	n/a	chr12:1105078-1105089
8	STAT3	chr12:1104582-1105094	MCF10A-Er-Src	breast:	n/a	chr12:1105078-1105089
9	FOS	chr12:1104663-1105272	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:1102489..1104981-chr12:1121749..1123712,2	MCF-7	breast:
2	chr12:1099800..1103499-chr12:1103569..1107416,6	MCF-7	breast:
3	chr12:1097166..1102781-chr12:1103327..1109862,10	MCF-7	breast:
4	chr12:1098824..1101586-chr12:1103414..1105051,2	K562	blood:

Variant related genes	Relation type
ENSG00000250132	TF binding region
ERC1	TF binding region
ENSG00000002016	Chromatin interaction
ENSG00000082805	Chromatin interaction
ENSG00000250132	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs11061617	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11064639	0.92[EUR][1000 genomes]
rs12309611	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12312678	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12319815	0.93[ASW][hapmap];0.89[CEU][hapmap];1.00[GIH][hapmap];0.85[LWK][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12322032	0.88[CEU][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12322480	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs16932151	0.83[LWK][hapmap]
rs28613628	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs34012460	0.93[EUR][1000 genomes]
rs61917245	0.95[EUR][1000 genomes]
rs61918704	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7954858	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7979798	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9630269	0.93[ASW][hapmap];0.89[CEU][hapmap];1.00[GIH][hapmap];0.85[LWK][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9668496	0.89[CEU][hapmap];0.91[GIH][hapmap];0.82[MEX][hapmap];0.86[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:28 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1049944	chr12:282465-1232077	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats 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	80 gene(s)	inside rSNPs	diseases
2	nsv541306	chr12:282465-1232077	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats 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	80 gene(s)	inside rSNPs	diseases
3	nsv949469	chr12:380411-1122450	Enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
4	nsv556892	chr12:673515-1210884	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
5	nsv898576	chr12:813411-1553450	Enhancers Genic enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
6	nsv948760	chr12:863833-1542875	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
7	nsv1052589	chr12:910460-1421493	ZNF genes & repeats Weak transcription Enhancers Active TSS Strong transcription 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	34 gene(s)	inside rSNPs	diseases
8	nsv1045278	chr12:920251-1697030	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS 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	46 gene(s)	inside rSNPs	diseases
9	nsv529398	chr12:941915-1741311	Weak transcription Strong transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
10	nsv468960	chr12:975276-1455106	Enhancers Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
11	nsv556941	chr12:975276-1455106	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
12	nsv1044329	chr12:985144-1403020	Genic enhancers Weak transcription Enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
13	nsv541340	chr12:985144-1403020	Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
14	nsv470256	chr12:998365-1438761	Enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
15	nsv492321	chr12:1011692-1388512	Weak transcription Active TSS Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
16	nsv898579	chr12:1013176-1510505	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
17	nsv898580	chr12:1024688-1569097	Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
18	nsv1036488	chr12:1041097-1445923	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
19	nsv1037825	chr12:1045734-1432940	Bivalent/Poised TSS Weak transcription Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
20	nsv541342	chr12:1045734-1432940	Active TSS Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
21	nsv868854	chr12:1045935-1354083	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
22	nsv468962	chr12:1047531-1119958	Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
23	nsv556942	chr12:1047531-1119958	Flanking Active TSS Weak transcription Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
24	esv2762958	chr12:1049279-1554962	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
25	nsv1052559	chr12:1077964-1588543	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS 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	29 gene(s)	inside rSNPs	diseases
26	nsv898581	chr12:1084783-1527359	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
27	nsv1041799	chr12:1091294-1304839	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
28	nsv541343	chr12:1091294-1304839	Flanking Active TSS Weak transcription Enhancers Genic enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:1101000-1123000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr12:1101200-1112800	Weak transcription	Gastric	stomach
3	chr12:1101200-1112800	Weak transcription	Ovary	ovary
4	chr12:1101200-1137000	Weak transcription	Lung	lung
5	chr12:1101400-1113000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr12:1101400-1115400	Weak transcription	Esophagus	oesophagus
7	chr12:1101600-1105600	Weak transcription	Left Ventricle	heart
8	chr12:1101600-1106200	Weak transcription	Brain Substantia Nigra	brain
9	chr12:1101600-1106600	Weak transcription	Skeletal Muscle Female	skeletal muscle
10	chr12:1101600-1107400	Weak transcription	HSMM	muscle
11	chr12:1101600-1109800	Weak transcription	Fetal Stomach	stomach
12	chr12:1101600-1112600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr12:1101600-1112800	Weak transcription	Primary T cells fromperipheralblood	blood
14	chr12:1101600-1112800	Weak transcription	Fetal Thymus	thymus
15	chr12:1101600-1112800	Weak transcription	Right Ventricle	heart
16	chr12:1101600-1112800	Weak transcription	Thymus	Thymus
17	chr12:1101600-1113200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr12:1101600-1116200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr12:1101600-1116200	Weak transcription	Small Intestine	intestine
20	chr12:1101600-1130400	Weak transcription	Fetal Muscle Trunk	muscle
21	chr12:1101600-1136800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr12:1101600-1136800	Weak transcription	Fetal Muscle Leg	muscle
23	chr12:1101600-1137000	Weak transcription	Rectal Mucosa Donor 31	rectum
24	chr12:1101800-1112800	Weak transcription	Right Atrium	heart
25	chr12:1101800-1131000	Weak transcription	Primary B cells from cord blood	blood
26	chr12:1102000-1106600	Weak transcription	Brain Anterior Caudate	brain
27	chr12:1102000-1106600	Weak transcription	Psoas Muscle	Psoas
28	chr12:1102000-1107400	Weak transcription	Duodenum Mucosa	Duodenum
29	chr12:1102000-1110400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr12:1102000-1110400	Weak transcription	Stomach Smooth Muscle	stomach
31	chr12:1102000-1112600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
32	chr12:1102000-1112800	Weak transcription	Brain Germinal Matrix	brain
33	chr12:1102000-1112800	Weak transcription	Fetal Intestine Small	intestine
34	chr12:1102000-1122800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr12:1102000-1137000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
36	chr12:1102000-1137200	Weak transcription	Fetal Lung	lung
37	chr12:1102200-1105200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr12:1102200-1106000	Weak transcription	Brain Cingulate Gyrus	brain
39	chr12:1102200-1106000	Weak transcription	Fetal Brain Female	brain
40	chr12:1102200-1106400	Weak transcription	Rectal Mucosa Donor 29	rectum
41	chr12:1102200-1106600	Weak transcription	Fetal Heart	heart
42	chr12:1102200-1107600	Weak transcription	Fetal Intestine Large	intestine
43	chr12:1102200-1110400	Weak transcription	HUES48 Cell Line	embryonic stem cell
44	chr12:1102200-1112400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr12:1102200-1112600	Weak transcription	HUES6 Cell Line	embryonic stem cell
46	chr12:1102200-1112600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr12:1102200-1112800	Weak transcription	Brain Hippocampus Middle	brain
48	chr12:1102200-1118800	Weak transcription	Fetal Brain Male	brain
49	chr12:1102200-1122600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr12:1102200-1129000	Weak transcription	Primary T cells from cord blood	blood

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