Variant report

Variant	rs17523988
Chromosome Location	chr12:39222785-39222786
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 44 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10506129	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10875979	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs10876086	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs10876149	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10876163	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11169169	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs11169301	0.95[AFR][1000 genomes]
rs11169387	1.00[ASW][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.87[ASN][1000 genomes]
rs11169508	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.95[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs11169511	0.95[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs11169547	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs11169666	0.95[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs11169769	1.00[CEU][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11169801	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11169879	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11169908	0.84[ASW][hapmap];0.87[CEU][hapmap];0.86[GIH][hapmap];0.97[TSI][hapmap];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11514111	0.80[ASN][1000 genomes]
rs11523607	0.82[ASN][1000 genomes]
rs11609849	0.96[CEU][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11610376	0.85[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs11612004	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.95[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs11613205	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11615668	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12812262	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs12827647	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1486357	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs1554550	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.95[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs1601579	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs17464772	0.96[CEU][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17465893	0.82[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap]
rs1843639	0.95[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs2056159	0.96[CEU][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2388060	0.84[ASW][hapmap];0.87[CEU][hapmap];0.86[GIH][hapmap];0.97[TSI][hapmap];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs34204495	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs36035670	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3886109	0.81[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs4332556	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6580755	1.00[ASW][hapmap];0.82[CHD][hapmap];0.85[MEX][hapmap];0.95[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs7301104	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs7960621	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7967776	0.87[CEU][hapmap];0.84[EUR][1000 genomes]
rs7973992	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AFR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1047623	chr12:39187817-39539939	Active TSS Bivalent Enhancer Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
2	esv3389115	chr12:39221256-39448458	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:39203200-39276000	Weak transcription	Aorta	Aorta
2	chr12:39204000-39284800	Weak transcription	Lung	lung
3	chr12:39204800-39228800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr12:39204800-39231800	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr12:39205600-39223200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr12:39205600-39229400	Weak transcription	HMEC	breast
7	chr12:39206400-39225800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr12:39206600-39243800	Weak transcription	Left Ventricle	heart
9	chr12:39206600-39249200	Weak transcription	Primary hematopoietic stem cells	blood
10	chr12:39206800-39226200	Weak transcription	GM12878-XiMat	blood
11	chr12:39206800-39241400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
12	chr12:39206800-39241400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr12:39216000-39237400	Weak transcription	Hela-S3	cervix
14	chr12:39217600-39232800	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr12:39218200-39223200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr12:39219200-39242600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr12:39219400-39229000	Weak transcription	Primary monocytes fromperipheralblood	blood
18	chr12:39221000-39223000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr12:39221600-39223800	Strong transcription	Monocytes-CD14+_RO01746	blood
20	chr12:39221800-39227800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
21	chr12:39221800-39251800	Weak transcription	Liver	Liver
22	chr12:39222000-39223200	Weak transcription	Pancreatic Islets	Pancreatic Islet

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