Variant report

Variant	rs10516151
Chromosome Location	chr5:178344648-178344649
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 54 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10035887	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10040956	0.87[CEU][hapmap];0.86[EUR][1000 genomes]
rs10043579	0.97[ASN][1000 genomes]
rs10044051	0.84[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs10055777	0.96[ASN][1000 genomes]
rs10055826	0.97[ASN][1000 genomes]
rs10067521	0.87[CEU][hapmap];0.87[EUR][1000 genomes]
rs10071186	0.93[ASN][1000 genomes]
rs10434800	0.87[ASN][1000 genomes]
rs1046726	0.91[CEU][hapmap];0.93[TSI][hapmap];0.87[EUR][1000 genomes]
rs10479515	0.87[CEU][hapmap];0.87[EUR][1000 genomes]
rs10479516	0.87[CEU][hapmap];0.87[EUR][1000 genomes]
rs11249601	0.97[ASN][1000 genomes]
rs11249603	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11743869	0.87[CEU][hapmap];0.87[EUR][1000 genomes]
rs11745403	0.86[CHB][hapmap];0.90[JPT][hapmap];0.94[ASN][1000 genomes]
rs11746382	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11955586	0.87[CEU][hapmap];0.93[TSI][hapmap];0.87[EUR][1000 genomes]
rs11960446	0.87[EUR][1000 genomes]
rs12653764	0.85[ASN][1000 genomes]
rs13154558	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13362387	0.86[CHB][hapmap];0.86[CHD][hapmap];0.91[JPT][hapmap]
rs1496949	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1496950	1.00[CEU][hapmap];0.89[YRI][hapmap];0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1995079	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2004503	0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs4130052	0.87[CEU][hapmap];0.86[EUR][1000 genomes]
rs4700927	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62393052	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6600990	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6600993	0.91[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs6600994	0.91[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs6866021	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6870709	0.85[EUR][1000 genomes]
rs6872605	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6872794	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6873993	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6880072	0.97[ASN][1000 genomes]
rs6885597	0.86[EUR][1000 genomes]
rs6897783	0.97[ASN][1000 genomes]
rs6898923	0.97[ASN][1000 genomes]
rs6899251	0.97[ASN][1000 genomes]
rs7701607	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7702579	0.86[EUR][1000 genomes]
rs7702879	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7718717	0.87[ASN][1000 genomes]
rs9329059	0.86[EUR][1000 genomes]
rs953740	0.86[AMR][1000 genomes];0.97[ASN][1000 genomes]

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	nsv883218	chr5:178219855-178349391	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv600464	chr5:178344648-178350709	ZNF genes & repeats Weak transcription Strong transcription	TF binding region lncRNA	1 gene(s)	inside rSNPs	diseases
3	nsv600465	chr5:178344648-178352002	ZNF genes & repeats Weak transcription Strong transcription	TF binding region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv600466	chr5:178344648-178352245	ZNF genes & repeats Weak transcription Strong transcription	TF binding region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv600467	chr5:178344648-178352820	ZNF genes & repeats Weak transcription Strong transcription	TF binding region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv600468	chr5:178344648-178353156	Weak transcription ZNF genes & repeats Strong transcription	TF binding region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs10516151	HNRNPAB	cis	parietal	SCAN
rs10516151	ZFP2	cis	cerebellum	SCAN
rs10516151	ZNF454	cis	parietal	SCAN
rs10516151	N4BP3	cis	parietal	SCAN

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:178335600-178349000	ZNF genes & repeats	Liver	Liver
2	chr5:178335800-178367000	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
3	chr5:178340400-178344800	Weak transcription	Fetal Brain Male	brain
4	chr5:178340400-178345400	Weak transcription	Placenta	Placenta
5	chr5:178341600-178345800	ZNF genes & repeats	Fetal Lung	lung
6	chr5:178341600-178345800	ZNF genes & repeats	Ovary	ovary
7	chr5:178341600-178347000	ZNF genes & repeats	Adipose Nuclei	Adipose
8	chr5:178341600-178347200	ZNF genes & repeats	Stomach Smooth Muscle	stomach
9	chr5:178341600-178367000	ZNF genes & repeats	Fetal Brain Female	brain
10	chr5:178342000-178348200	Weak transcription	Right Ventricle	heart
11	chr5:178342200-178345000	Weak transcription	Fetal Heart	heart
12	chr5:178342800-178346000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr5:178343000-178346000	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
14	chr5:178343000-178367200	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
15	chr5:178343400-178345600	Weak transcription	Psoas Muscle	Psoas
16	chr5:178343600-178344800	Weak transcription	Colon Smooth Muscle	Colon
17	chr5:178343600-178345000	Strong transcription	Brain Hippocampus Middle	brain
18	chr5:178343800-178344800	Weak transcription	Primary T cells from cord blood	blood
19	chr5:178343800-178344800	Weak transcription	Aorta	Aorta
20	chr5:178343800-178345200	Weak transcription	Skeletal Muscle Female	skeletal muscle
21	chr5:178343800-178345400	Weak transcription	Brain Germinal Matrix	brain
22	chr5:178343800-178345400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr5:178343800-178345400	Weak transcription	Left Ventricle	heart
24	chr5:178343800-178348000	Weak transcription	Brain Angular Gyrus	brain
25	chr5:178344000-178344800	Weak transcription	Brain Inferior Temporal Lobe	brain
26	chr5:178344000-178344800	Weak transcription	Brain Substantia Nigra	brain
27	chr5:178344000-178344800	Weak transcription	Skeletal Muscle Male	skeletal muscle
28	chr5:178344200-178344800	Strong transcription	Fetal Stomach	stomach
29	chr5:178344200-178345000	Weak transcription	Fetal Kidney	kidney

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