Variant report

Variant	rs7132146
Chromosome Location	chr12:25305350-25305351
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	USF1	chr12:25305088-25305352	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr12:25303736-25305364	IMR90	lung:	n/a	n/a

Variant related genes	Relation type
CASC1	TF binding region

Extended variants
information (count: 52 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10743543	1.00[CEU][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10771172	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10842474	0.90[CEU][hapmap];0.81[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10842479	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10842480	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10842481	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10842482	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10842484	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10842485	0.88[ASW][hapmap];1.00[CEU][hapmap];0.95[GIH][hapmap];0.98[MKK][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10842486	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10842513	1.00[CHD][hapmap]
rs11047853	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11047863	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11047864	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12313024	0.85[CEU][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1979522	1.00[CHD][hapmap]
rs2200402	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2200408	1.00[CEU][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2220193	1.00[CEU][hapmap];0.95[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2220195	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4246226	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4280085	1.00[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4291763	1.00[CEU][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4418900	1.00[CEU][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4427639	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4441109	0.83[ASW][hapmap];0.97[MKK][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes]
rs4460902	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4491339	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[TSI][hapmap];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4963854	1.00[CEU][hapmap];0.81[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55746605	1.00[ASN][1000 genomes]
rs57579413	1.00[ASN][1000 genomes]
rs60110571	1.00[ASN][1000 genomes]
rs61391424	1.00[ASN][1000 genomes]
rs7133919	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7298884	1.00[CEU][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7299464	1.00[CEU][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7303889	1.00[CHD][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7488357	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7957575	1.00[CEU][hapmap];1.00[GIH][hapmap];0.96[TSI][hapmap];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7959689	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7966074	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7966158	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7966255	1.00[CEU][hapmap];0.98[EUR][1000 genomes];1.00[ASN][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:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:25304000-25305400	Enhancers	Muscle Satellite Cultured Cells	--
2	chr12:25304000-25305400	Enhancers	NHLF	lung
3	chr12:25304000-25305800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr12:25304000-25307400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr12:25304200-25305400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr12:25304200-25305400	Enhancers	HMEC	breast
7	chr12:25304200-25305400	Enhancers	NH-A	brain
8	chr12:25304400-25305400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr12:25304400-25305400	Enhancers	Fetal Lung	lung
10	chr12:25304400-25305400	Enhancers	Fetal Stomach	stomach
11	chr12:25304400-25305400	Enhancers	NHEK	skin
12	chr12:25304400-25305600	Enhancers	HUES48 Cell Line	embryonic stem cell
13	chr12:25304400-25305600	Enhancers	iPS-20b Cell Line	embryonic stem cell
14	chr12:25304400-25305800	Enhancers	ES-I3 Cell Line	embryonic stem cell
15	chr12:25304400-25305800	Enhancers	H9 Cell Line	embryonic stem cell
16	chr12:25304400-25305800	Enhancers	HUES6 Cell Line	embryonic stem cell
17	chr12:25304400-25305800	Enhancers	iPS-18 Cell Line	embryonic stem cell
18	chr12:25304600-25305800	Enhancers	H1 Cell Line	embryonic stem cell
19	chr12:25304600-25305800	Enhancers	HUES64 Cell Line	embryonic stem cell
20	chr12:25304600-25305800	Enhancers	iPS-15b Cell Line	embryonic stem cell
21	chr12:25304600-25315600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr12:25304800-25305400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
23	chr12:25304800-25305400	Enhancers	Hela-S3	cervix
24	chr12:25305000-25305600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr12:25305000-25305600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr12:25305000-25308000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr12:25305200-25307600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr12:25305200-25307800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr12:25305200-25307800	Weak transcription	Duodenum Smooth Muscle	Duodenum
30	chr12:25305200-25307800	Weak transcription	NHDF-Ad	bronchial
31	chr12:25305200-25308000	Weak transcription	A549	lung
32	chr12:25305200-25308200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links