Variant report

Variant	rs10187424
Chromosome Location	chr2:85794297-85794298
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:85792131..85794386-chr2:85795797..85798233,4	K562	blood:
2	chr2:85765001..85768151-chr2:85794146..85798905,4	K562	blood:
3	chr2:85792880..85794386-chr2:85796161..85797994,2	K562	blood:

Variant related genes	Relation type
ENSG00000168906	Chromatin interaction

Extended variants
information (count: 67 )
Associated
traits (count: 19 )

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs1009	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap]
rs1010	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1011	0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10172544	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10175792	0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs10176176	0.89[ASN][1000 genomes]
rs10179195	0.91[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10198569	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10206961	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs1058588	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1078004	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.80[AFR][1000 genomes];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11891260	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12473819	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12714145	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13394343	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13411109	0.83[AMR][1000 genomes]
rs1348818	0.81[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs1446669	0.82[CHB][hapmap];0.81[CHD][hapmap];0.85[JPT][hapmap]
rs1561198	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1562323	0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17026396	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1972297	0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2028898	0.86[CHB][hapmap];0.80[CHD][hapmap];0.85[JPT][hapmap]
rs2028900	0.82[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.85[MKK][hapmap];0.81[YRI][hapmap];0.90[ASN][1000 genomes]
rs2043675	0.86[CHB][hapmap];0.81[CHD][hapmap];0.85[JPT][hapmap]
rs2044474	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2166529	0.81[CHB][hapmap]
rs2232748	0.80[JPT][hapmap]
rs2289972	0.86[CHB][hapmap]
rs2366639	0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2592551	0.86[CHB][hapmap];0.83[CHD][hapmap];0.85[JPT][hapmap]
rs2886722	0.92[CEU][hapmap];0.81[CHB][hapmap];0.84[TSI][hapmap]
rs35215812	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35565292	0.87[AMR][1000 genomes]
rs3731827	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3731828	0.86[CHB][hapmap];0.82[CHD][hapmap]
rs3755014	0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3755015	0.85[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3770098	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs55971080	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs59877521	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6547620	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6547621	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6547624	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6547629	0.80[JPT][hapmap]
rs6705839	0.85[ASN][1000 genomes]
rs6705971	0.85[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6714157	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6714709	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6721924	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6731005	0.87[ASN][1000 genomes]
rs6733550	0.80[JPT][hapmap]
rs6733913	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6735152	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6738645	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6739015	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6743030	0.88[ASN][1000 genomes]
rs6750832	0.80[ASN][1000 genomes]
rs6750847	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6757263	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs699664	0.86[CHB][hapmap];0.83[CHD][hapmap];0.85[JPT][hapmap]
rs7568458	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7579147	0.86[CHB][hapmap]
rs7591175	0.81[CHB][hapmap]
rs7593969	0.86[CHB][hapmap];0.83[CHD][hapmap]
rs7605975	0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs762684	0.86[CHB][hapmap];0.85[JPT][hapmap]

Variant related diseases (count:1)

Disease	PMID	Source
Prostate cancer	21743467	GWAS catalog

mRNA abundance (count:18)

SNP	Gene	Cis/trans	Tissue	Source
rs10187424	VAMP8	cis	Esophagus Mucosa	GTEx
rs10187424	GGCX	cis	Artery Aorta	GTEx
rs10187424	LOC388969	cis	multi-tissue	Pritchard
rs10187424	VAMP8	cis	uninvolved skin	skin_eQTL
rs10187424	GGCX	cis	Artery Tibial	GTEx
rs10187424	VAMP8	cis	lesional skin	skin_eQTL
rs10187424	VAMP8	cis	lymphoblastoid	seeQTL
rs10187424	VAMP8	Cis_1M	lymphoblastoid	RTeQTL
rs10187424	VAMP8	cis	multi-tissue	Pritchard
rs10187424	GGCX	cis	Nerve Tibial	GTEx
rs10187424	GGCX	cis	multi-tissue	Pritchard
rs10187424	GGCX	cis	parietal	SCAN
rs10187424	GGCX	cis	cerebellum	SCAN
rs10187424	MAT2A	cis	cerebellum	SCAN
rs10187424	VAMP8	cis	parietal	SCAN
rs10187424	GGCX	Cis_1M	lymphoblastoid	RTeQTL
rs10187424	RNF103	cis	parietal	SCAN
rs10187424	GGCX	cis	Whole Blood	GTEx

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:85789400-85797400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr2:85789400-85803400	Weak transcription	Adipose Nuclei	Adipose
3	chr2:85789400-85803400	Weak transcription	Right Atrium	heart
4	chr2:85789400-85804000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr2:85789600-85797600	Weak transcription	Placenta	Placenta
6	chr2:85791200-85795200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr2:85791600-85799800	Weak transcription	K562	blood

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