Variant report

Variant	rs12810577
Chromosome Location	chr12:25346163-25346164
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:25343757..25346723-chr12:25347243..25349142,2	K562	blood:

Variant related genes	Relation type
ENSG00000205707	Chromatin interaction
ENSG00000118307	Chromatin interaction

Extended variants
information (count: 103 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:97)

rs_ID	r²[population]
rs10505960	0.90[ASW][hapmap];0.92[CEU][hapmap];0.84[CHB][hapmap];0.90[CHD][hapmap];0.86[GIH][hapmap];0.92[JPT][hapmap];0.88[MEX][hapmap];0.86[MKK][hapmap];0.95[TSI][hapmap];0.81[AMR][1000 genomes]
rs10505980	0.84[CHD][hapmap];0.92[JPT][hapmap]
rs10771177	0.83[EUR][1000 genomes]
rs10842466	0.89[CHB][hapmap]
rs10842473	0.81[AMR][1000 genomes]
rs10842475	0.82[AMR][1000 genomes]
rs10842492	0.96[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10842494	0.84[CHB][hapmap];0.91[JPT][hapmap]
rs10842496	0.84[CHD][hapmap];0.92[JPT][hapmap]
rs10842498	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10842499	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10842501	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs10842502	0.94[CHB][hapmap];0.92[JPT][hapmap];0.84[ASN][1000 genomes]
rs10842504	0.94[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs10842505	1.00[CHB][hapmap];0.91[JPT][hapmap];0.84[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs10842512	0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs10842514	0.90[ASW][hapmap];0.80[CHD][hapmap];0.92[JPT][hapmap];0.92[MEX][hapmap]
rs11047824	0.89[CHB][hapmap]
rs11047854	0.84[AMR][1000 genomes]
rs11047855	0.84[AMR][1000 genomes]
rs11047856	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11047865	0.96[CEU][hapmap];0.83[CHB][hapmap];0.92[JPT][hapmap];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11047887	0.83[ASW][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs11047888	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs11047894	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs11047895	0.84[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs11047896	0.84[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs11047897	0.84[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs11047901	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs11047902	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs11047905	0.90[ASN][1000 genomes]
rs11047909	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11047915	0.92[JPT][hapmap]
rs11047919	0.80[CHD][hapmap];0.92[JPT][hapmap];0.84[MEX][hapmap]
rs1137188	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs1137189	0.84[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs1137196	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11513449	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11608657	0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs11611468	1.00[CHB][hapmap];0.84[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs11832421	0.89[CHB][hapmap]
rs12226937	0.92[JPT][hapmap]
rs12245	0.84[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs12368504	1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs12423443	0.88[CEU][hapmap];0.84[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];0.92[JPT][hapmap];0.98[TSI][hapmap]
rs12424283	0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs12424685	0.82[AMR][1000 genomes]
rs12578773	0.84[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs12579073	1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs12579681	0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs12579942	1.00[CHB][hapmap];0.87[CHD][hapmap];0.92[JPT][hapmap];0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs12580030	0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs12581134	0.80[AMR][1000 genomes]
rs12581706	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12587	1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs12813551	0.80[CHD][hapmap];0.92[JPT][hapmap]
rs12814442	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12815546	1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs12818169	0.84[AMR][1000 genomes]
rs12820019	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12822857	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs12828609	0.84[AMR][1000 genomes]
rs12830058	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12830336	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs13096	1.00[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs17329025	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.96[MEX][hapmap];0.94[MKK][hapmap];0.98[TSI][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1908946	0.89[CHB][hapmap]
rs2291365	0.92[CEU][hapmap];0.84[CHB][hapmap];0.87[CHD][hapmap];0.86[GIH][hapmap];0.92[JPT][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap]
rs2352782	0.92[CEU][hapmap];0.84[CHB][hapmap];0.97[CHD][hapmap];0.86[GIH][hapmap];0.92[JPT][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap];0.82[AMR][1000 genomes]
rs2352784	0.82[AMR][1000 genomes]
rs34898174	0.82[EUR][1000 genomes]
rs4246228	0.84[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs4246229	1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs4494384	0.84[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs4551857	0.84[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs4559767	0.90[ASW][hapmap];0.96[CEU][hapmap];0.84[CHB][hapmap];0.97[CHD][hapmap];0.86[GIH][hapmap];0.92[JPT][hapmap];0.88[MEX][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes]
rs4963859	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs4963860	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs4963861	0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs5009909	0.88[ASN][1000 genomes]
rs61020746	0.81[AMR][1000 genomes]
rs6487461	0.84[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs6487464	0.81[CHD][hapmap];0.92[JPT][hapmap]
rs712	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs7137630	0.89[ASN][1000 genomes]
rs7297103	0.84[CEU][hapmap];0.84[CHB][hapmap];0.87[CHD][hapmap];0.81[GIH][hapmap];0.92[JPT][hapmap];0.87[TSI][hapmap]
rs7298636	0.90[JPT][hapmap]
rs7299998	0.84[CHB][hapmap];0.90[CHD][hapmap];0.92[JPT][hapmap]
rs7302922	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs7303094	0.81[ASN][1000 genomes]
rs7306769	0.84[CHB][hapmap];0.90[CHD][hapmap];0.92[JPT][hapmap]
rs7308865	0.84[CHB][hapmap];0.91[JPT][hapmap]
rs7312739	0.84[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs7955844	0.84[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs8720	0.84[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs9266	1.00[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs9634100	0.84[CHB][hapmap];0.92[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 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	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12810577	LYRM5	cis	parietal	SCAN
rs12810577	GOLT1B	cis	parietal	SCAN

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:25340200-25347400	Weak transcription	Liver	Liver
2	chr12:25341000-25347200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr12:25341000-25347200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
4	chr12:25341000-25347400	Weak transcription	Primary T helper cells PMA-I stimulated	--
5	chr12:25341000-25347400	Weak transcription	HMEC	breast
6	chr12:25341200-25346800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
7	chr12:25341200-25347400	Weak transcription	NHEK	skin
8	chr12:25341400-25347600	Weak transcription	HSMMtube	muscle
9	chr12:25341800-25347400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr12:25342000-25347200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr12:25342000-25347400	Weak transcription	A549	lung
12	chr12:25342400-25347200	Weak transcription	Rectal Smooth Muscle	rectum
13	chr12:25342400-25347600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr12:25342600-25347000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr12:25342800-25347200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr12:25342800-25347200	Weak transcription	Hela-S3	cervix
17	chr12:25342800-25347600	Weak transcription	NH-A	brain
18	chr12:25343000-25347200	Weak transcription	Osteobl	bone
19	chr12:25343000-25347600	Weak transcription	NHLF	lung
20	chr12:25343200-25347400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr12:25345600-25347000	Weak transcription	Brain Anterior Caudate	brain

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