Variant report

Variant	rs10198569
Chromosome Location	chr2:85794415-85794416
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:85765001..85768151-chr2:85794146..85798905,4	K562	blood:

Variant related genes	Relation type
ENSG00000168906	Chromatin interaction

Extended variants
information (count: 67 )
Associated
traits (count: 14 )

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];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1011	0.97[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	0.88[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]
rs10187424	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];0.97[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[AMR][1000 genomes];0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11891260	0.82[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	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13411109	0.81[AMR][1000 genomes]
rs1348818	0.81[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs1446669	0.82[CHB][hapmap];0.83[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];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1562323	0.97[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];0.87[MKK][hapmap];0.98[TSI][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1972297	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2028898	0.86[CHB][hapmap];0.82[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];0.88[LWK][hapmap];0.81[YRI][hapmap];0.90[ASN][1000 genomes]
rs2043675	0.86[CHB][hapmap];0.83[CHD][hapmap];0.85[JPT][hapmap]
rs2044474	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[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	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2592551	0.86[CHB][hapmap];0.85[CHD][hapmap];0.85[JPT][hapmap]
rs2886722	0.92[CEU][hapmap];0.81[CHB][hapmap];0.84[TSI][hapmap]
rs35215812	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35565292	0.85[AMR][1000 genomes]
rs3731827	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3731828	0.86[CHB][hapmap];0.84[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];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs55971080	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs59877521	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6547620	0.92[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];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6547624	0.98[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	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6721924	0.90[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	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6735152	0.89[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];0.81[AFR][1000 genomes];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6739015	0.92[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	0.90[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];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs699664	0.86[CHB][hapmap];0.85[CHD][hapmap];0.85[JPT][hapmap]
rs7568458	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.81[AFR][1000 genomes];0.87[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];0.85[CHD][hapmap]
rs7605975	0.80[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs762684	0.86[CHB][hapmap];0.85[JPT][hapmap]

mRNA abundance (count:14)

SNP	Gene	Cis/trans	Tissue	Source
rs10198569	GGCX	cis	Artery Aorta	GTEx
rs10198569	GGCX	cis	Whole Blood	GTEx
rs10198569	RNF103	cis	parietal	SCAN
rs10198569	GGCX	cis	cerebellum	SCAN
rs10198569	GGCX	cis	Nerve Tibial	GTEx
rs10198569	VAMP8	cis	multi-tissue	Pritchard
rs10198569	VAMP8	cis	lymphoblastoid	seeQTL
rs10198569	MAT2A	cis	cerebellum	SCAN
rs10198569	VAMP8	Cis_1M	lymphoblastoid	RTeQTL
rs10198569	VAMP8	cis	Esophagus Mucosa	GTEx
rs10198569	GGCX	cis	Artery Tibial	GTEx
rs10198569	GGCX	Cis_1M	lymphoblastoid	RTeQTL
rs10198569	VAMP8	cis	parietal	SCAN
rs10198569	GGCX	cis	parietal	SCAN

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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