Variant report

Variant	rs4987313
Chromosome Location	chr1:169672360-169672361
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 28 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs11581878	1.00[CEU][hapmap];1.00[TSI][hapmap]
rs12034295	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12036824	1.00[ASW][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs12036888	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12038025	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12038193	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12038568	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12038818	0.91[AFR][1000 genomes]
rs12041598	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2272915	0.90[YRI][hapmap]
rs2298901	1.00[CEU][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3917391	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3917421	1.00[CEU][hapmap];0.82[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3917724	1.00[MEX][hapmap]
rs4363475	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4987276	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4987278	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4987282	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4987330	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4987332	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4987333	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4987342	1.00[CEU][hapmap];0.89[GIH][hapmap];0.92[EUR][1000 genomes]
rs7526937	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532586	chr1:169593222-169713184	Weak transcription Transcr. at gene 5' and 3' Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	esv3451367	chr1:169630075-169976964	Strong transcription Flanking Active TSS Genic enhancers Enhancers Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	nsv872539	chr1:169658586-169674590	Weak transcription Genic enhancers Transcr. at gene 5' and 3' Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv1009313	chr1:169661299-169680173	Transcr. at gene 5' and 3' Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv872541	chr1:169672360-169695815	Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Enhancers Bivalent Enhancer Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4987313	WNT5A	trans	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:169662400-169676000	Genic enhancers	Primary B cells from peripheral blood	blood
2	chr1:169663200-169674000	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
3	chr1:169664000-169673400	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr1:169664000-169674000	Genic enhancers	Fetal Thymus	thymus
5	chr1:169664000-169674200	Genic enhancers	Primary T cells fromperipheralblood	blood
6	chr1:169666200-169673800	Genic enhancers	Primary T helper cells fromperipheralblood	blood
7	chr1:169667600-169673600	Genic enhancers	Primary neutrophils fromperipheralblood	blood
8	chr1:169667600-169676800	Genic enhancers	Primary monocytes fromperipheralblood	blood
9	chr1:169668000-169677400	Transcr. at gene 5' and 3'	Primary T cells from cord blood	blood
10	chr1:169669400-169673000	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
11	chr1:169669600-169672800	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
12	chr1:169669600-169674400	Genic enhancers	Primary hematopoietic stem cells	blood
13	chr1:169670000-169673600	Weak transcription	GM12878-XiMat	blood
14	chr1:169670200-169673200	Genic enhancers	Primary T helper naive cells from peripheral blood	blood
15	chr1:169670600-169678000	Transcr. at gene 5' and 3'	Primary T helper cells PMA-I stimulated	--
16	chr1:169670800-169672800	Transcr. at gene 5' and 3'	Primary T helper naive cells fromperipheralblood	blood
17	chr1:169671000-169672600	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
18	chr1:169671000-169673600	Genic enhancers	Primary mononuclear cells fromperipheralblood	Blood
19	chr1:169671000-169675000	Genic enhancers	Monocytes-CD14+_RO01746	blood
20	chr1:169671200-169673600	Genic enhancers	Primary T killer naive cells fromperipheralblood	blood
21	chr1:169671200-169679400	Transcr. at gene 5' and 3'	Dnd41	blood
22	chr1:169671400-169673200	Genic enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr1:169671600-169673400	Genic enhancers	Primary T helper memory cells from peripheral blood 1	blood
24	chr1:169671800-169673600	Genic enhancers	Primary T killer memory cells from peripheral blood	blood
25	chr1:169672000-169672600	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr1:169672000-169672800	Weak transcription	Thymus	Thymus
27	chr1:169672000-169672800	Strong transcription	Spleen	Spleen
28	chr1:169672000-169673200	Genic enhancers	Primary B cells from cord blood	blood
29	chr1:169672200-169672800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood

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