Variant report

Variant	rs6544180
Chromosome Location	chr2:39135927-39135928
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 46 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs1010858	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1010859	0.84[TSI][hapmap];0.81[EUR][1000 genomes]
rs10181808	0.86[EUR][1000 genomes]
rs10204999	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10779923	0.89[CHB][hapmap];0.87[CHD][hapmap];0.80[ASN][1000 genomes]
rs11124654	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11124655	0.95[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs1131752	0.81[EUR][1000 genomes]
rs11689954	0.84[CEU][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12617734	0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs12621073	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12712625	0.81[GIH][hapmap]
rs12712627	0.81[GIH][hapmap];0.85[MKK][hapmap]
rs12712628	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13035182	0.95[EUR][1000 genomes]
rs17422748	0.89[EUR][1000 genomes]
rs1868867	0.81[ASN][1000 genomes]
rs1901289	0.88[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];0.92[JPT][hapmap];0.94[MKK][hapmap];0.94[ASN][1000 genomes]
rs2060743	0.88[CHB][hapmap]
rs2373473	0.81[CEU][hapmap]
rs3099940	0.88[CEU][hapmap];0.82[EUR][1000 genomes]
rs3099941	0.88[CEU][hapmap];0.91[GIH][hapmap];0.85[TSI][hapmap];0.82[EUR][1000 genomes]
rs3099942	0.87[CEU][hapmap];0.91[GIH][hapmap];0.96[TSI][hapmap];0.85[EUR][1000 genomes]
rs3099945	0.84[CEU][hapmap];0.88[GIH][hapmap]
rs3099957	0.80[EUR][1000 genomes]
rs3099958	0.80[CEU][hapmap];0.89[EUR][1000 genomes]
rs3099959	0.96[CEU][hapmap];0.94[CHB][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3099998	0.82[EUR][1000 genomes]
rs373300	0.85[CEU][hapmap];0.86[GIH][hapmap];0.91[MEX][hapmap];0.86[MKK][hapmap];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs384007	0.82[EUR][1000 genomes]
rs384421	0.84[EUR][1000 genomes]
rs389023	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs390008	0.81[ASN][1000 genomes]
rs4265996	0.83[CHB][hapmap];0.80[ASN][1000 genomes]
rs434696	0.83[EUR][1000 genomes]
rs4670267	0.83[CHB][hapmap];0.96[CHD][hapmap];0.92[JPT][hapmap];0.90[ASN][1000 genomes]
rs4670268	0.84[CEU][hapmap];0.88[EUR][1000 genomes]
rs4670899	0.92[CEU][hapmap];0.88[CHB][hapmap];0.89[GIH][hapmap];0.86[MEX][hapmap];0.85[MKK][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6706091	1.00[CEU][hapmap];0.88[CHB][hapmap];0.92[JPT][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6706186	0.80[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs6738069	0.84[CEU][hapmap];0.82[GIH][hapmap];0.81[MEX][hapmap];0.84[TSI][hapmap];0.87[EUR][1000 genomes]
rs6744514	0.92[CEU][hapmap];0.88[CHB][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6754902	0.97[EUR][1000 genomes]
rs7598922	0.81[GIH][hapmap];0.89[MKK][hapmap]
rs8179664	0.84[EUR][1000 genomes]
rs9808136	0.92[CEU][hapmap];0.87[CHB][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs6544180	ITGB1	trans	parietal	SCAN
rs6544180	DHX57	Cis_1M	lymphoblastoid	RTeQTL
rs6544180	MORN2	cis	parietal	SCAN
rs6544180	DHX57	cis	cerebellum	SCAN

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:39110200-39186800	Weak transcription	Stomach Smooth Muscle	stomach
2	chr2:39132000-39136200	Enhancers	HepG2	liver
3	chr2:39132400-39136400	Enhancers	Breast Myoepithelial Primary Cells	Breast
4	chr2:39134000-39137000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
5	chr2:39134400-39136000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr2:39135000-39136400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
7	chr2:39135200-39136000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr2:39135400-39136600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
9	chr2:39135600-39136200	Flanking Active TSS	GM12878-XiMat	blood

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