Variant report

Variant	rs486836
Chromosome Location	chr1:150875967-150875968
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 30 )
Associated
traits (count: 22 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs1081512	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11204725	0.96[CEU][hapmap];0.82[EUR][1000 genomes]
rs11204735	1.00[CEU][hapmap];0.86[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs11204737	1.00[CEU][hapmap];0.88[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs1136774	0.81[EUR][1000 genomes]
rs12125650	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs12126004	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12402006	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12404199	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12410050	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12568757	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs12758227	0.92[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs2039590	0.82[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs2089081	0.90[EUR][1000 genomes]
rs2305814	0.81[CHB][hapmap];0.80[JPT][hapmap]
rs267735	0.81[ASN][1000 genomes]
rs3754211	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4970932	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4970976	0.86[EUR][1000 genomes]
rs6587551	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6694531	0.89[CEU][hapmap]
rs7412746	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7532008	0.81[CHB][hapmap]
rs7534124	0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2829859	chr1:150608894-150937329	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
2	nsv1001897	chr1:150743271-151241600	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
3	nsv535158	chr1:150743271-151241600	Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
4	nsv2810	chr1:150835173-150879869	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
5	nsv1008496	chr1:150845827-150970656	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
6	nsv946385	chr1:150875504-150878115	Weak transcription Enhancers	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:22)

SNP	Gene	Cis/trans	Tissue	Source
rs486836	ARNT	cis	multi-tissue	Pritchard
rs486836	HORMAD1	cis	Nerve Tibial	GTEx
rs486836	RP11-316M1.12	cis	Thyroid	GTEx
rs486836	RP11-316M1.12	cis	Skin Sun Exposed Lower leg	GTEx
rs486836	RNU6-1042P	cis	Esophagus Mucosa	GTEx
rs486836	RP11-316M1.12	cis	Artery Tibial	GTEx
rs486836	CTSK	Cis_1M	lymphoblastoid	RTeQTL
rs486836	RP11-316M1.12	cis	Nerve Tibial	GTEx
rs486836	ARNT	cis	normal skin	skin_eQTL
rs486836	HORMAD1	cis	Esophagus Mucosa	GTEx
rs486836	HORMAD1	cis	Skin Sun Exposed Lower leg	GTEx
rs486836	ARNT	cis	uninvolved skin	skin_eQTL
rs486836	ARNT	Cis_1M	lymphoblastoid	RTeQTL
rs486836	CTSS	Cis_1M	lymphoblastoid	RTeQTL
rs486836	CTSK	cis	multi-tissue	Pritchard
rs486836	RP11-316M1.12	cis	Muscle Skeletal	GTEx
rs486836	RP11-316M1.12	cis	lung	GTEx
rs486836	RP11-316M1.12	cis	Adipose Subcutaneous	GTEx
rs486836	HORMAD1	cis	lesional skin	skin_eQTL
rs486836	RP11-316M1.12	cis	Esophagus Muscularis	GTEx
rs486836	RP11-316M1.12	cis	Whole Blood	GTEx
rs486836	HORMAD1	cis	uninvolved skin	skin_eQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:150875400-150879000	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr1:150875600-150876600	Enhancers	Placenta	Placenta

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