Variant report

Variant	rs7624185
Chromosome Location	chr3:160695770-160695771
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 76 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs10154889	0.95[CEU][hapmap];0.90[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs10433352	0.81[CEU][hapmap];0.81[JPT][hapmap];0.81[MEX][hapmap];0.88[TSI][hapmap];0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11711152	1.00[CEU][hapmap];0.83[GIH][hapmap];0.80[JPT][hapmap];0.91[TSI][hapmap]
rs11713093	0.95[JPT][hapmap];0.83[YRI][hapmap];0.91[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs11715733	0.91[AMR][1000 genomes]
rs11717272	0.90[CEU][hapmap];0.84[CHD][hapmap];0.85[GIH][hapmap];0.90[MEX][hapmap];0.88[TSI][hapmap];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11718966	1.00[CEU][hapmap];0.85[JPT][hapmap]
rs11720263	0.90[CEU][hapmap];0.82[CHD][hapmap];0.85[GIH][hapmap];0.95[MEX][hapmap];0.88[TSI][hapmap];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11916355	0.87[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs11922957	0.87[AMR][1000 genomes]
rs11922959	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12696112	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12696113	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13060718	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13062651	0.87[AMR][1000 genomes]
rs13071892	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs13071999	0.89[ASW][hapmap];1.00[CEU][hapmap];0.95[GIH][hapmap];0.80[JPT][hapmap];0.84[MEX][hapmap];0.94[TSI][hapmap];0.82[EUR][1000 genomes]
rs13073059	1.00[CEU][hapmap];0.80[JPT][hapmap];0.82[EUR][1000 genomes]
rs13085336	0.90[CEU][hapmap]
rs13098896	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13256	0.90[CEU][hapmap];0.86[CHD][hapmap];0.88[GIH][hapmap];0.95[MEX][hapmap];0.88[TSI][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13315565	0.94[CEU][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1345156	1.00[CEU][hapmap];0.97[GIH][hapmap];0.84[MEX][hapmap];0.94[TSI][hapmap];0.83[EUR][1000 genomes]
rs1374787	0.82[CHD][hapmap];0.81[JPT][hapmap];0.86[MEX][hapmap]
rs1447610	1.00[ASW][hapmap];1.00[CEU][hapmap];0.88[GIH][hapmap];0.80[JPT][hapmap];0.85[MEX][hapmap];0.94[TSI][hapmap]
rs1447622	1.00[CEU][hapmap]
rs1562464	1.00[ASW][hapmap];1.00[CEU][hapmap];0.84[CHD][hapmap];0.97[GIH][hapmap];0.85[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1599388	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs16831796	0.81[CEU][hapmap];0.88[TSI][hapmap];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs16831886	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1868105	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs1868107	1.00[CEU][hapmap];0.83[GIH][hapmap];0.80[JPT][hapmap];0.91[TSI][hapmap]
rs2014810	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2044571	1.00[CEU][hapmap];0.85[JPT][hapmap];0.94[YRI][hapmap];0.91[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs2889390	0.95[CHB][hapmap];0.95[JPT][hapmap];0.98[ASN][1000 genomes]
rs34630898	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs35914913	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4494975	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4521287	0.90[CEU][hapmap];0.86[CHD][hapmap];0.85[GIH][hapmap];0.95[MEX][hapmap];0.88[TSI][hapmap];0.89[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs4679920	1.00[CEU][hapmap];0.84[JPT][hapmap]
rs4679929	0.89[AMR][1000 genomes]
rs57145341	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6441338	1.00[CEU][hapmap];0.85[JPT][hapmap]
rs6768115	1.00[CEU][hapmap];0.80[JPT][hapmap];0.91[TSI][hapmap]
rs6772723	0.90[CEU][hapmap];0.90[MEX][hapmap];0.88[TSI][hapmap]
rs6774725	1.00[CEU][hapmap];0.88[TSI][hapmap]
rs6794882	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6801444	1.00[CEU][hapmap]
rs6806015	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs68166680	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs73021215	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs73023235	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7433918	0.81[AMR][1000 genomes]
rs7610432	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7618924	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7628389	0.81[CEU][hapmap];0.84[CHD][hapmap];0.81[MEX][hapmap];0.88[TSI][hapmap];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7641892	1.00[CEU][hapmap];0.85[JPT][hapmap]
rs898677	0.81[CEU][hapmap];0.82[CHD][hapmap];0.81[MEX][hapmap];0.88[TSI][hapmap];0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs935497	1.00[ASW][hapmap];1.00[CEU][hapmap];0.88[GIH][hapmap];0.80[JPT][hapmap];0.85[MEX][hapmap];0.94[TSI][hapmap]
rs964533	1.00[CEU][hapmap];0.81[JPT][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9812507	1.00[CEU][hapmap];0.81[JPT][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9822435	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.88[YRI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9832109	1.00[CEU][hapmap];0.82[CHD][hapmap];0.83[GIH][hapmap];0.81[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9844267	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[GIH][hapmap];0.80[JPT][hapmap];0.91[TSI][hapmap]
rs9845943	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[GIH][hapmap];0.91[TSI][hapmap]
rs9857482	1.00[CEU][hapmap]
rs9857855	0.84[CEU][hapmap];0.81[JPT][hapmap];0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9860537	1.00[CEU][hapmap];0.97[GIH][hapmap];0.97[LWK][hapmap];0.89[MEX][hapmap];0.94[MKK][hapmap];0.97[TSI][hapmap];0.83[YRI][hapmap];0.85[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs9862086	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9871801	0.82[EUR][1000 genomes]
rs9876142	0.90[CEU][hapmap];0.82[CHB][hapmap];0.89[CHD][hapmap];0.88[GIH][hapmap];0.85[JPT][hapmap];0.90[MEX][hapmap];0.88[TSI][hapmap];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9880269	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9883566	0.90[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];0.90[GIH][hapmap];0.90[JPT][hapmap];0.90[MEX][hapmap];0.91[TSI][hapmap];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532666	chr3:159777847-160703202	Enhancers Weak transcription ZNF genes & repeats Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	271 gene(s)	inside rSNPs	diseases
2	nsv931072	chr3:160669567-161159779	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
3	nsv1007004	chr3:160695108-160718154	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs7624185	B3GALNT1	cis	lymphoblastoid	seeQTL
rs7624185	PPM1L	cis	cerebellum	SCAN
rs7624185	SPTSSB	cis	Thyroid	GTEx
rs7624185	C3orf57	cis	parietal	SCAN

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:160667400-160696000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
2	chr3:160670400-160700400	Weak transcription	Skeletal Muscle Female	skeletal muscle
3	chr3:160678400-160697600	Weak transcription	Primary T cells from cord blood	blood
4	chr3:160687000-160696600	Weak transcription	Right Ventricle	heart
5	chr3:160687000-160698600	Weak transcription	Adipose Nuclei	Adipose
6	chr3:160691600-160697800	Weak transcription	Primary hematopoietic stem cells	blood
7	chr3:160695000-160696800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr3:160695200-160695800	Enhancers	Monocytes-CD14+_RO01746	blood
9	chr3:160695200-160696200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr3:160695200-160696200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr3:160695200-160698600	Enhancers	Primary neutrophils fromperipheralblood	blood
12	chr3:160695200-160701400	Enhancers	Primary monocytes fromperipheralblood	blood
13	chr3:160695600-160695800	Enhancers	Primary hematopoietic stem cells short term culture	blood

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