Variant report

Variant	rs3782688
Chromosome Location	chr12:31451505-31451506
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	TBP	chr12:31451361-31452092	GM12878	blood:	n/a	chr12:31451363-31451374
2	RELA	chr12:31451429-31451873	GM18526	blood:	n/a	n/a
3	RELA	chr12:31451244-31451996	GM18951	blood:	n/a	n/a
4	EBF1	chr12:31451443-31451978	GM12878	blood:	n/a	n/a
5	POLR2A	chr12:31450910-31451777	GM12878	blood:	n/a	n/a
6	RELA	chr12:31450620-31452165	GM12878	blood:	n/a	n/a
7	NFIC	chr12:31451386-31451928	GM12878	blood:	n/a	n/a
8	MXI1	chr12:31450640-31451932	GM12878	blood:	n/a	n/a
9	MTA3	chr12:31450653-31451551	GM12878	blood:	n/a	n/a
10	POLR2A	chr12:31451280-31452142	K562	blood:	n/a	n/a
11	FOXM1	chr12:31450614-31451891	GM12878	blood:	n/a	n/a
12	EP300	chr12:31450726-31451812	GM12878	blood:	n/a	chr12:31450747-31450756
13	RELA	chr12:31450667-31451867	GM19193	blood:	n/a	n/a
14	RUNX3	chr12:31450521-31451867	GM12878	blood:	n/a	chr12:31450740-31450749 chr12:31450740-31450749
15	RELA	chr12:31450688-31451970	GM10847	blood:	n/a	n/a
16	TBL1XR1	chr12:31450651-31452021	GM12878	blood:	n/a	n/a
17	FOXM1	chr12:31450954-31451766	GM12878	blood:	n/a	n/a
18	POLR2A	chr12:31451400-31451615	H1-hESC	embryonic stem cell:	n/a	n/a
19	POU2F2	chr12:31451420-31451737	GM12878	blood:	n/a	chr12:31451551-31451558 chr12:31451544-31451566 chr12:31451549-31451559 chr12:31451547-31451562 chr12:31451548-31451560 chr12:31451546-31451564 chr12:31451550-31451559
20	RELA	chr12:31450613-31452128	GM19099	blood:	n/a	n/a
21	STAT3	chr12:31450740-31452127	GM12878	blood:	n/a	chr12:31450750-31450757
22	RELA	chr12:31450618-31452065	GM12891	blood:	n/a	n/a
23	BHLHE40	chr12:31450670-31451865	GM12878	blood:	n/a	n/a
24	E2F4	chr12:31451388-31451586	MCF10A-Er-Src	breast:	n/a	n/a
25	POLR2A	chr12:31450894-31451972	GM12878	blood:	n/a	n/a
26	POLR2A	chr12:31451339-31451554	HepG2	liver:	n/a	n/a
27	POU2F2	chr12:31451354-31451747	GM12878	blood:	n/a	chr12:31451551-31451558 chr12:31451544-31451566 chr12:31451549-31451559 chr12:31451547-31451562 chr12:31451548-31451560 chr12:31451546-31451564 chr12:31451550-31451559
28	RELA	chr12:31450693-31452188	GM18505	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:31449423..31452288-chr12:31476341..31478296,3	MCF-7	breast:
2	chr12:31450718..31452727-chr12:31455647..31457589,2	K562	blood:
3	chr12:31447793..31455081-chr12:31455286..31461328,11	K562	blood:
4	chr12:31449879..31452217-chr12:31476391..31478263,2	MCF-7	breast:

Variant related genes	Relation type
FAM60A	TF binding region
ENSG00000139146	Chromatin interaction
ENSG00000177340	Chromatin interaction
ENSG00000238661	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10843918	1.00[EUR][1000 genomes]
rs11051394	1.00[EUR][1000 genomes]
rs11051395	1.00[EUR][1000 genomes]
rs11051396	1.00[EUR][1000 genomes]
rs11051399	1.00[EUR][1000 genomes]
rs11051402	1.00[EUR][1000 genomes]
rs11051403	1.00[EUR][1000 genomes]
rs11051409	1.00[EUR][1000 genomes]
rs12226982	1.00[EUR][1000 genomes]
rs12228674	1.00[EUR][1000 genomes]
rs12581740	1.00[EUR][1000 genomes]
rs17576073	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17576094	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17576143	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17576150	0.81[CHB][hapmap];0.80[CHD][hapmap];0.85[JPT][hapmap]
rs17603871	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs17603906	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17603947	0.81[CHB][hapmap]
rs2293039	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2293040	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3741872	0.84[CHD][hapmap];0.90[GIH][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3741873	0.84[CHD][hapmap];0.90[GIH][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4930974	0.81[CHB][hapmap];0.80[CHD][hapmap];0.85[JPT][hapmap];0.81[ASN][1000 genomes]
rs57061710	1.00[EUR][1000 genomes]
rs60022875	1.00[EUR][1000 genomes]
rs7301494	1.00[EUR][1000 genomes]
rs9971805	0.81[CHB][hapmap];0.80[CHD][hapmap];0.85[JPT][hapmap];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:18 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1041877	chr12:31009451-31809254	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription 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 miRNA target site	71 gene(s)	inside rSNPs	diseases
2	nsv541440	chr12:31009451-31809254	ZNF genes & repeats Enhancers Strong transcription Weak transcription Genic enhancers Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
3	esv2758303	chr12:31125467-31491104	Active TSS Strong transcription Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Genic enhancers 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	51 gene(s)	inside rSNPs	diseases
4	esv2759890	chr12:31125467-31491104	Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
5	nsv428276	chr12:31125467-31491104	Strong transcription Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
6	esv2751043	chr12:31148662-31499671	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
7	esv2751046	chr12:31174233-31684733	Bivalent Enhancer Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
8	nsv515974	chr12:31201717-31452750	Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
9	nsv1045497	chr12:31213735-31458547	ZNF genes & repeats Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
10	esv2751053	chr12:31225710-31484881	Active TSS Weak transcription Bivalent/Poised TSS Strong transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
11	esv2754121	chr12:31225710-31493435	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
12	esv2751054	chr12:31225710-31513718	Strong transcription ZNF genes & repeats Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
13	esv35092	chr12:31239600-31484833	Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Weak transcription Enhancers Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
14	esv2751071	chr12:31239600-31493435	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
15	esv2751072	chr12:31239600-31499671	Bivalent/Poised TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
16	nsv430477	chr12:31239600-31513718	Flanking Bivalent TSS/Enh Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
17	esv2751077	chr12:31278031-31499671	Active TSS Flanking Active TSS Strong transcription Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
18	nsv524737	chr12:31399901-31464663	Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:31426000-31460200	Weak transcription	Aorta	Aorta
2	chr12:31427200-31459800	Weak transcription	Gastric	stomach
3	chr12:31427600-31460800	Strong transcription	Fetal Thymus	thymus
4	chr12:31428600-31458600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr12:31428600-31470000	Weak transcription	Small Intestine	intestine
6	chr12:31430600-31462200	Weak transcription	Psoas Muscle	Psoas
7	chr12:31430800-31460600	Weak transcription	Right Ventricle	heart
8	chr12:31433000-31470200	Weak transcription	Stomach Mucosa	stomach
9	chr12:31434000-31456200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr12:31434600-31459800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr12:31435600-31458200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
12	chr12:31435600-31460600	Strong transcription	Dnd41	blood
13	chr12:31436200-31455400	Weak transcription	Fetal Brain Male	brain
14	chr12:31437600-31453000	Strong transcription	Thymus	Thymus
15	chr12:31438400-31459600	Strong transcription	Hela-S3	cervix
16	chr12:31439000-31453800	Weak transcription	Pancreatic Islets	Pancreatic Islet
17	chr12:31440200-31457600	Weak transcription	Brain Germinal Matrix	brain
18	chr12:31440200-31460000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr12:31440400-31453200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr12:31440400-31462200	Weak transcription	Osteobl	bone
21	chr12:31440800-31470000	Weak transcription	Fetal Lung	lung
22	chr12:31441200-31455400	Weak transcription	Ovary	ovary
23	chr12:31441600-31452800	Strong transcription	H1 Cell Line	embryonic stem cell
24	chr12:31441600-31453800	Weak transcription	Spleen	Spleen
25	chr12:31442200-31451600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr12:31442600-31452800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
27	chr12:31442600-31453800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
28	chr12:31442600-31453800	Strong transcription	HUES6 Cell Line	embryonic stem cell
29	chr12:31443600-31454000	Strong transcription	A549	lung
30	chr12:31444000-31452800	Strong transcription	Monocytes-CD14+_RO01746	blood
31	chr12:31444000-31458400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr12:31445200-31452000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
33	chr12:31445400-31460000	Weak transcription	Left Ventricle	heart
34	chr12:31445800-31459000	Strong transcription	K562	blood
35	chr12:31446200-31460400	Weak transcription	Brain Anterior Caudate	brain
36	chr12:31446600-31458200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr12:31446600-31468000	Weak transcription	Fetal Heart	heart
38	chr12:31446600-31470000	Weak transcription	Muscle Satellite Cultured Cells	--
39	chr12:31447400-31452200	Strong transcription	ES-I3 Cell Line	embryonic stem cell
40	chr12:31447800-31456200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
41	chr12:31448000-31456200	Weak transcription	Adipose Nuclei	Adipose
42	chr12:31448000-31456200	Weak transcription	Fetal Brain Female	brain
43	chr12:31448000-31456400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr12:31448000-31457800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr12:31448000-31468000	Weak transcription	Placenta Amnion	Placenta Amnion
46	chr12:31448200-31455200	Weak transcription	Placenta	Placenta
47	chr12:31448200-31455400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
48	chr12:31448200-31456800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
49	chr12:31448400-31453800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr12:31448400-31455400	Weak transcription	Fetal Kidney	kidney

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