Variant report

Variant	rs4313666
Chromosome Location	chr12:25304707-25304708
allele	A/G
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	ATF1	chr12:25304482-25304710	K562	blood:	n/a	n/a
2	JUND	chr12:25304094-25304967	SK-N-SH	brain:	n/a	chr12:25304564-25304573
3	FOS	chr12:25304424-25304771	MCF10A-Er-Src	breast:	n/a	chr12:25304564-25304573
4	FOS	chr12:25304491-25304760	MCF10A-Er-Src	breast:	n/a	chr12:25304564-25304573
5	POLR2A	chr12:25303736-25305364	IMR90	lung:	n/a	n/a
6	MAFK	chr12:25304407-25304914	IMR90	lung:	n/a	n/a
7	RAD21	chr12:25304347-25304954	IMR90	lung:	n/a	n/a
8	RCOR1	chr12:25303920-25305060	IMR90	lung:	n/a	n/a
9	CEBPB	chr12:25304380-25304975	IMR90	lung:	n/a	n/a
10	FOS	chr12:25304444-25304789	MCF10A-Er-Src	breast:	n/a	chr12:25304564-25304573
11	JUND	chr12:25304422-25304730	HepG2	liver:	n/a	chr12:25304564-25304573
12	JUN	chr12:25304410-25304828	HUVEC	blood vessel:	n/a	chr12:25304564-25304573 chr12:25304560-25304573
13	KAP1	chr12:25304400-25304880	HEK293	kidney:	n/a	n/a
14	POLR2A	chr12:25304342-25304723	SK-N-SH	brain:	n/a	n/a
15	E2F4	chr12:25304638-25304814	MCF10A-Er-Src	breast:	n/a	n/a
16	FOS	chr12:25304442-25304738	MCF10A-Er-Src	breast:	n/a	chr12:25304564-25304573

Variant related genes	Relation type
CASC1	TF binding region

Extended variants
information (count: 74 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs10505959	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs10771166	0.88[CHB][hapmap]
rs10771171	0.83[ASN][1000 genomes]
rs10771174	0.90[CHB][hapmap];0.83[JPT][hapmap]
rs10771175	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10771176	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10842464	0.88[CHB][hapmap]
rs10842468	0.90[JPT][hapmap]
rs10842470	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10842472	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10842476	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10842483	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10842488	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10842490	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs10842491	0.92[ASN][1000 genomes]
rs10842495	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10842515	0.88[CEU][hapmap];1.00[JPT][hapmap]
rs10842516	0.90[CEU][hapmap];0.90[JPT][hapmap]
rs10842517	0.90[CEU][hapmap];0.90[JPT][hapmap]
rs11047843	0.85[EUR][1000 genomes]
rs11047852	0.83[ASN][1000 genomes]
rs11047858	0.81[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11047862	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11047878	0.82[AMR][1000 genomes]
rs11047879	0.82[AMR][1000 genomes]
rs11047885	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes]
rs11047912	1.00[JPT][hapmap]
rs11047914	0.90[CEU][hapmap];0.91[JPT][hapmap]
rs11047917	0.91[JPT][hapmap]
rs11834088	0.88[CHB][hapmap]
rs12227966	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12228638	1.00[CHB][hapmap];0.89[JPT][hapmap];0.82[ASN][1000 genomes]
rs12367971	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17388587	1.00[JPT][hapmap]
rs17389103	0.88[CEU][hapmap];1.00[JPT][hapmap]
rs2220196	0.90[CEU][hapmap];0.89[CHB][hapmap];0.90[JPT][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2883030	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3924650	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4368021	0.88[CEU][hapmap];1.00[JPT][hapmap]
rs4589388	0.82[ASN][1000 genomes]
rs4963859	0.82[JPT][hapmap]
rs55950027	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6487458	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7133640	0.89[CEU][hapmap];0.91[JPT][hapmap]
rs7134616	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs7135130	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7303373	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7303669	1.00[CHB][hapmap]
rs7309670	0.81[CEU][hapmap];0.89[JPT][hapmap]
rs7315339	1.00[JPT][hapmap]
rs7956818	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7960428	0.89[CHB][hapmap]
rs7960917	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7964623	0.82[AMR][1000 genomes]
rs7965763	0.82[AMR][1000 genomes]
rs7971062	0.89[CHB][hapmap];0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs7971288	1.00[CHB][hapmap];0.89[JPT][hapmap];0.82[ASN][1000 genomes]
rs7973365	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7973450	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7973623	0.94[CEU][hapmap];0.82[AMR][1000 genomes]
rs7975271	1.00[CHB][hapmap]
rs7976254	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs7976355	0.85[JPT][hapmap]
rs7980769	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes]
rs7980834	0.82[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv469169	chr12:24692383-25357680	Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Weak transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	nsv557775	chr12:24692383-25357680	Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv932477	chr12:24705151-25346677	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Bivalent TSS/Enh 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	30 gene(s)	inside rSNPs	diseases
4	nsv1067577	chr12:24791283-25346677	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats 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	22 gene(s)	inside rSNPs	diseases
5	nsv529514	chr12:24791283-25346677	Enhancers Weak transcription Strong transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers 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	22 gene(s)	inside rSNPs	diseases
6	nsv557796	chr12:25266203-25306458	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
7	nsv515612	chr12:25272027-25341177	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
8	nsv557797	chr12:25272027-25341177	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
9	nsv898922	chr12:25274593-25408047	Genic enhancers Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:25304000-25305200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr12:25304000-25305400	Enhancers	Muscle Satellite Cultured Cells	--
3	chr12:25304000-25305400	Enhancers	NHLF	lung
4	chr12:25304000-25305800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr12:25304000-25307400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr12:25304200-25305000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr12:25304200-25305200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr12:25304200-25305200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr12:25304200-25305200	Enhancers	NHDF-Ad	bronchial
10	chr12:25304200-25305200	Enhancers	Osteobl	bone
11	chr12:25304200-25305400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr12:25304200-25305400	Enhancers	HMEC	breast
13	chr12:25304200-25305400	Enhancers	NH-A	brain
14	chr12:25304400-25304800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr12:25304400-25305000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr12:25304400-25305000	Enhancers	Stomach Smooth Muscle	stomach
17	chr12:25304400-25305200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr12:25304400-25305200	Enhancers	A549	lung
19	chr12:25304400-25305200	Enhancers	HUVEC	blood vessel
20	chr12:25304400-25305400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr12:25304400-25305400	Enhancers	Fetal Lung	lung
22	chr12:25304400-25305400	Enhancers	Fetal Stomach	stomach
23	chr12:25304400-25305400	Enhancers	NHEK	skin
24	chr12:25304400-25305600	Enhancers	HUES48 Cell Line	embryonic stem cell
25	chr12:25304400-25305600	Enhancers	iPS-20b Cell Line	embryonic stem cell
26	chr12:25304400-25305800	Enhancers	ES-I3 Cell Line	embryonic stem cell
27	chr12:25304400-25305800	Enhancers	H9 Cell Line	embryonic stem cell
28	chr12:25304400-25305800	Enhancers	HUES6 Cell Line	embryonic stem cell
29	chr12:25304400-25305800	Enhancers	iPS-18 Cell Line	embryonic stem cell
30	chr12:25304600-25305000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr12:25304600-25305000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr12:25304600-25305000	Enhancers	Fetal Kidney	kidney
33	chr12:25304600-25305000	Enhancers	HSMM	muscle
34	chr12:25304600-25305800	Enhancers	H1 Cell Line	embryonic stem cell
35	chr12:25304600-25305800	Enhancers	HUES64 Cell Line	embryonic stem cell
36	chr12:25304600-25305800	Enhancers	iPS-15b Cell Line	embryonic stem cell
37	chr12:25304600-25315600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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