Variant report

Variant	rs12578995
Chromosome Location	chr12:47554862-47554863
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 47 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10785658	0.90[CEU][hapmap];0.83[EUR][1000 genomes]
rs10785660	0.89[CHB][hapmap];0.90[JPT][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10785661	0.83[CEU][hapmap];0.85[CHB][hapmap];0.85[TSI][hapmap];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10881051	0.83[CEU][hapmap]
rs10881056	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10881057	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10881058	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11183755	0.90[CEU][hapmap];0.83[EUR][1000 genomes]
rs11183769	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11183774	0.90[CEU][hapmap];0.83[MEX][hapmap];0.85[TSI][hapmap];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12371765	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12578367	0.83[CEU][hapmap]
rs12579796	0.83[CEU][hapmap]
rs12830116	0.82[CEU][hapmap]
rs1357933	1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1357935	0.95[CEU][hapmap];0.88[GIH][hapmap];0.88[MEX][hapmap];0.95[TSI][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1404812	0.83[CEU][hapmap]
rs1404819	0.83[CEU][hapmap]
rs1525444	0.90[CEU][hapmap];0.82[EUR][1000 genomes]
rs1525453	0.82[CEU][hapmap];0.90[CHB][hapmap];0.80[JPT][hapmap];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1830054	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1880600	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.90[YRI][hapmap];0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1917658	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1949864	0.90[CEU][hapmap];0.84[EUR][1000 genomes]
rs2091294	0.83[CEU][hapmap]
rs2408714	0.90[CEU][hapmap]
rs4768141	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4768775	0.83[CEU][hapmap]
rs4768777	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs55651541	0.85[EUR][1000 genomes]
rs6582696	0.90[CEU][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7135951	0.89[CEU][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7136496	0.85[AMR][1000 genomes]
rs7295263	0.82[CEU][hapmap];0.80[EUR][1000 genomes]
rs7297792	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7299627	0.80[EUR][1000 genomes]
rs7311824	0.82[ASW][hapmap];0.86[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap];0.82[LWK][hapmap];0.92[MEX][hapmap];0.88[TSI][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7313938	0.83[AFR][1000 genomes]
rs7958186	0.90[CEU][hapmap];0.84[EUR][1000 genomes]
rs7958922	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7963822	0.90[CEU][hapmap];0.84[EUR][1000 genomes]
rs7974123	0.84[EUR][1000 genomes]
rs9634260	0.90[CEU][hapmap];0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv469368	chr12:47374908-47675680	Enhancers Genic enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
2	nsv558784	chr12:47374908-47675680	Genic enhancers Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	nsv832399	chr12:47502910-47689601	Genic enhancers Enhancers Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
4	esv2751100	chr12:47541390-47746157	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:47536000-47578000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr12:47536200-47564200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr12:47541600-47558400	Weak transcription	NHEK	skin
4	chr12:47550400-47558000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
5	chr12:47550400-47558200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
6	chr12:47550400-47558400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr12:47550400-47560000	Weak transcription	Adipose Nuclei	Adipose
8	chr12:47550400-47562200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr12:47550600-47556200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
10	chr12:47550600-47556400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr12:47550600-47558200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
12	chr12:47550600-47558400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr12:47550600-47558400	Weak transcription	Ovary	ovary
14	chr12:47550600-47558400	Weak transcription	Right Atrium	heart
15	chr12:47550600-47571800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
16	chr12:47550600-47582400	Weak transcription	Aorta	Aorta
17	chr12:47550800-47557400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
18	chr12:47550800-47560000	Weak transcription	Duodenum Smooth Muscle	Duodenum
19	chr12:47550800-47570000	Weak transcription	Colon Smooth Muscle	Colon
20	chr12:47550800-47570200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
21	chr12:47551200-47557400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
22	chr12:47551200-47557800	Weak transcription	Primary T helper cells fromperipheralblood	blood
23	chr12:47551200-47583600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr12:47551400-47557600	Weak transcription	Pancreas	Pancrea
25	chr12:47551400-47567200	Weak transcription	Spleen	Spleen
26	chr12:47551800-47556200	Weak transcription	Primary T helper cells PMA-I stimulated	--
27	chr12:47552800-47555400	ZNF genes & repeats	Primary T cells from cord blood	blood
28	chr12:47553800-47555400	Weak transcription	Primary T cells fromperipheralblood	blood
29	chr12:47554200-47555000	Enhancers	Primary monocytes fromperipheralblood	blood
30	chr12:47554400-47555000	Enhancers	Monocytes-CD14+_RO01746	blood
31	chr12:47554600-47555000	Enhancers	Primary B cells from peripheral blood	blood
32	chr12:47554600-47555000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
33	chr12:47554600-47558400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr12:47554800-47556200	Weak transcription	Primary B cells from cord blood	blood
35	chr12:47554800-47579600	Weak transcription	Primary T killer memory cells from peripheral blood	blood

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