Variant report

Variant	rs12058974
Chromosome Location	chr1:86192235-86192236
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 56 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs1047893	0.87[CEU][hapmap];0.86[CHB][hapmap];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1047895	0.80[CEU][hapmap]
rs10873716	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10873717	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11161649	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs11161650	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11161651	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11161654	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11161656	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11161657	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11161658	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11161659	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11161660	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11161661	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11161662	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs11161663	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11161664	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11161665	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11161667	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12063702	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12067749	0.87[AFR][1000 genomes]
rs12089500	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12097932	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12564080	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12566746	0.88[CEU][hapmap];0.87[CHB][hapmap];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12738010	0.87[ASN][1000 genomes]
rs12739713	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs12752817	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12756013	0.85[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs12757270	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs12758511	0.87[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs1539444	0.88[CEU][hapmap];0.86[CHB][hapmap];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1764285	0.80[CEU][hapmap]
rs1775988	0.80[CEU][hapmap]
rs1889919	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1889920	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2069208	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs2389972	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35438778	0.83[ASN][1000 genomes]
rs3753786	0.88[CEU][hapmap];0.86[CHB][hapmap];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3753789	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3753790	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6576784	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs6672312	0.88[CEU][hapmap];0.86[CHB][hapmap];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6689168	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6697535	0.88[CEU][hapmap];0.87[CHB][hapmap];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7518312	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs7520491	0.88[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.84[ASN][1000 genomes]
rs7532758	0.80[CEU][hapmap]
rs7554844	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs821386	0.80[CEU][hapmap]
rs821389	0.80[CEU][hapmap]

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	nsv1006994	chr1:85454304-86327679	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	esv3391173	chr1:86005637-86337469	Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
3	nsv817212	chr1:86127851-86658426	Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv871471	chr1:86143084-86211516	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs12058974	C1orf181	cis	multi-tissue	Pritchard
rs12058974	ZNHIT6	cis	lung	GTEx
rs12058974	ZNHIT6	cis	Artery Aorta	GTEx
rs12058974	ZNHIT6	cis	Esophagus Muscularis	GTEx
rs12058974	ZNHIT6	cis	Adipose Subcutaneous	GTEx
rs12058974	C1orf181	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:86190800-86194400	Weak transcription	Primary hematopoietic stem cells	blood
2	chr1:86191600-86210400	Weak transcription	Fetal Lung	lung

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