Variant report

Variant	rs4495966
Chromosome Location	chr12:10307590-10307591
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 50 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs1050283	0.91[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MKK][hapmap];0.86[TSI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1050286	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10505755	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10845051	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs10845054	0.88[ASN][1000 genomes]
rs10845056	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11053641	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11053643	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11053644	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11053647	0.84[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11053648	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11053649	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11053650	0.96[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs11053651	0.97[ASN][1000 genomes]
rs11053654	0.89[CEU][hapmap];0.86[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11608874	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11609310	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11615002	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11615035	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11831267	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12230161	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12231585	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12819932	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12822177	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13306593	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17174597	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17174598	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2171602	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2537777	0.93[JPT][hapmap]
rs2537778	0.93[JPT][hapmap]
rs2537779	0.93[JPT][hapmap]
rs2634164	0.86[ASN][1000 genomes]
rs34874375	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34908088	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35547206	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3736232	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3736233	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3736234	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3736235	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3816844	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3994135	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4482119	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4482120	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4495967	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4764299	0.89[CEU][hapmap];0.89[GIH][hapmap];0.93[JPT][hapmap];0.83[MEX][hapmap];0.82[TSI][hapmap];0.82[AMR][1000 genomes]
rs6488265	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs7296800	0.92[JPT][hapmap]
rs7300650	0.93[JPT][hapmap]
rs7315498	0.93[JPT][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv898757	chr12:10229281-10614641	Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs4495966	LOH12CR1	cis	cerebellum	SCAN
rs4495966	TAS2R19	cis	parietal	SCAN
rs4495966	GAPDH	cis	parietal	SCAN
rs4495966	OLR1	cis	multi-tissue	Pritchard
rs4495966	EMG1	cis	cerebellum	SCAN

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:10306400-10313400	Weak transcription	Hela-S3	cervix
2	chr12:10307000-10308200	Weak transcription	Primary neutrophils fromperipheralblood	blood
3	chr12:10307000-10309200	Weak transcription	Thymus	Thymus
4	chr12:10307000-10311400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
5	chr12:10307000-10312400	Weak transcription	Placenta	Placenta
6	chr12:10307000-10312800	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr12:10307000-10313400	Weak transcription	Brain Anterior Caudate	brain
8	chr12:10307000-10318600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr12:10307000-10319800	Weak transcription	Right Atrium	heart
10	chr12:10307200-10311000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr12:10307200-10311200	Weak transcription	Primary hematopoietic stem cells	blood
12	chr12:10307200-10311400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr12:10307400-10308200	Weak transcription	Primary monocytes fromperipheralblood	blood
14	chr12:10307400-10311400	Weak transcription	Monocytes-CD14+_RO01746	blood

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