Variant report

Variant	rs2089079
Chromosome Location	chr4:100451197-100451198
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	chr4:100449160..100451370-chr4:100870396..100872457,2	K562	blood:
2	chr4:100446974..100449213-chr4:100450825..100453764,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000245322	Chromatin interaction
ENSG00000164032	Chromatin interaction

Extended variants
information (count: 85 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:81)

rs_ID	r²[population]
rs10000018	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10007794	0.93[CEU][hapmap];0.88[EUR][1000 genomes]
rs10008896	0.89[EUR][1000 genomes]
rs10008928	0.89[EUR][1000 genomes]
rs10009198	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10019266	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10020461	0.94[CEU][hapmap];0.86[EUR][1000 genomes]
rs10026790	0.95[CEU][hapmap];0.93[GIH][hapmap];0.80[TSI][hapmap];0.85[EUR][1000 genomes]
rs10030937	0.95[CEU][hapmap];0.97[GIH][hapmap];0.89[EUR][1000 genomes]
rs10031512	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10516443	0.89[EUR][1000 genomes]
rs10516444	0.95[CEU][hapmap];0.86[EUR][1000 genomes]
rs1054730	0.89[EUR][1000 genomes]
rs1057615	0.85[EUR][1000 genomes]
rs11933250	0.94[CEU][hapmap];0.85[EUR][1000 genomes]
rs11933520	0.95[CEU][hapmap];0.84[EUR][1000 genomes]
rs11933937	0.84[EUR][1000 genomes]
rs11935581	0.86[EUR][1000 genomes]
rs11937107	0.85[EUR][1000 genomes]
rs11937273	0.85[EUR][1000 genomes]
rs11941470	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11943031	0.94[CEU][hapmap];0.84[EUR][1000 genomes]
rs11944752	0.95[CEU][hapmap];0.93[GIH][hapmap];0.80[TSI][hapmap];0.85[EUR][1000 genomes]
rs11946292	0.88[EUR][1000 genomes]
rs11946367	0.89[EUR][1000 genomes]
rs11946658	0.95[CEU][hapmap];0.85[EUR][1000 genomes]
rs11947558	0.84[EUR][1000 genomes]
rs1491235	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.90[MEX][hapmap];0.93[MKK][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1503774	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1503778	0.88[CEU][hapmap];0.85[EUR][1000 genomes]
rs17029108	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17598226	0.85[EUR][1000 genomes]
rs1800591	0.85[EUR][1000 genomes]
rs1800803	0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs1800804	0.95[CEU][hapmap];0.95[GIH][hapmap];0.80[TSI][hapmap];0.85[EUR][1000 genomes]
rs1873516	0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs1873517	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28368786	0.85[EUR][1000 genomes]
rs28376611	0.85[EUR][1000 genomes]
rs28431971	0.83[EUR][1000 genomes]
rs28435607	0.85[EUR][1000 genomes]
rs28444681	0.90[EUR][1000 genomes]
rs28473262	0.84[EUR][1000 genomes]
rs28497720	0.85[EUR][1000 genomes]
rs28500697	0.88[EUR][1000 genomes]
rs28595160	0.85[EUR][1000 genomes]
rs28608631	0.88[EUR][1000 genomes]
rs28621060	0.88[EUR][1000 genomes]
rs28647519	0.85[EUR][1000 genomes]
rs2866164	0.85[EUR][1000 genomes]
rs28666735	0.85[EUR][1000 genomes]
rs28678377	0.84[EUR][1000 genomes]
rs28704064	0.85[EUR][1000 genomes]
rs28789770	0.84[EUR][1000 genomes]
rs28849180	0.84[EUR][1000 genomes]
rs2903201	0.89[EUR][1000 genomes]
rs3811800	0.90[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs3816873	0.95[CEU][hapmap];0.95[GIH][hapmap];0.80[TSI][hapmap];0.85[EUR][1000 genomes]
rs4423880	0.89[EUR][1000 genomes]
rs6532820	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6815231	0.89[EUR][1000 genomes]
rs6839296	0.85[EUR][1000 genomes]
rs6841211	0.84[EUR][1000 genomes]
rs72681967	0.90[EUR][1000 genomes]
rs7656665	0.84[EUR][1000 genomes]
rs7661453	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7661656	0.89[EUR][1000 genomes]
rs7661665	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7661964	0.84[EUR][1000 genomes]
rs7682548	0.84[EUR][1000 genomes]
rs7686425	0.89[EUR][1000 genomes]
rs7687762	0.95[CEU][hapmap];0.85[EUR][1000 genomes]
rs7693203	0.84[EUR][1000 genomes]
rs7693979	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs867380	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs867381	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs884274	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs884275	0.90[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9307240	0.95[CEU][hapmap];0.84[EUR][1000 genomes]
rs9990558	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9997840	0.93[CEU][hapmap];0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv879656	chr4:99976646-100533722	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	esv3584519	chr4:100323870-100477462	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	esv3584522	chr4:100432841-100467011	Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	esv3584523	chr4:100437553-100476549	Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2089079	ADH6	cis	parietal	SCAN
rs2089079	C4orf37	cis	cerebellum	SCAN

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:100449800-100451200	Enhancers	Fetal Intestine Large	intestine
2	chr4:100449800-100451200	Enhancers	Fetal Muscle Leg	muscle
3	chr4:100449800-100451200	Enhancers	HSMMtube	muscle
4	chr4:100449800-100451400	Enhancers	Fetal Lung	lung
5	chr4:100450400-100451200	Enhancers	Colon Smooth Muscle	Colon
6	chr4:100451000-100451400	Enhancers	Stomach Mucosa	stomach

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