Variant report

Variant	rs12126004
Chromosome Location	chr1:150889877-150889878
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:150888318..150890863-chr1:150893491..150895097,2	K562	blood:
2	chr1:150887871..150890031-chr1:150893806..150895331,2	MCF-7	breast:
3	chr1:150888096..150891022-chr1:150892225..150894393,2	K562	blood:

Extended variants
information (count: 32 )
Associated
traits (count: 22 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs1081512	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11204725	0.96[CEU][hapmap];0.91[YRI][hapmap];0.81[EUR][1000 genomes]
rs11204735	1.00[CEU][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs11204737	1.00[CEU][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs1136774	0.80[EUR][1000 genomes]
rs11587718	0.80[CHB][hapmap];0.84[YRI][hapmap]
rs12125650	1.00[CEU][hapmap];0.91[YRI][hapmap];0.84[EUR][1000 genomes]
rs12402006	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12404199	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12410050	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12568757	1.00[CEU][hapmap]
rs12758227	0.86[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs1673160	0.84[YRI][hapmap]
rs1722784	0.91[YRI][hapmap]
rs2039590	0.88[EUR][1000 genomes]
rs2089081	0.89[EUR][1000 genomes]
rs2305814	0.85[CHB][hapmap]
rs267733	0.83[YRI][hapmap]
rs267735	0.83[ASN][1000 genomes]
rs3754211	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs486836	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4970932	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4970976	0.85[EUR][1000 genomes]
rs6587551	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7412746	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7532008	0.85[CHB][hapmap]
rs7534124	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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	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
5	nsv947130	chr1:150878115-150899504	Active TSS Flanking Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:22)

SNP	Gene	Cis/trans	Tissue	Source
rs12126004	ARNT	Cis_1M	lymphoblastoid	RTeQTL
rs12126004	HORMAD1	cis	Nerve Tibial	GTEx
rs12126004	CTSS	Cis_1M	lymphoblastoid	RTeQTL
rs12126004	RP11-316M1.12	cis	Whole Blood	GTEx
rs12126004	ARNT	cis	multi-tissue	Pritchard
rs12126004	RP11-316M1.12	cis	lung	GTEx
rs12126004	HORMAD1	cis	lesional skin	skin_eQTL
rs12126004	RP11-316M1.12	cis	Skin Sun Exposed Lower leg	GTEx
rs12126004	RP11-316M1.12	cis	Adipose Subcutaneous	GTEx
rs12126004	RP11-316M1.12	cis	Nerve Tibial	GTEx
rs12126004	RP11-316M1.12	cis	Artery Tibial	GTEx
rs12126004	HORMAD1	cis	uninvolved skin	skin_eQTL
rs12126004	CTSK	cis	multi-tissue	Pritchard
rs12126004	RNU6-1042P	cis	Esophagus Mucosa	GTEx
rs12126004	ARNT	cis	normal skin	skin_eQTL
rs12126004	ARNT	cis	uninvolved skin	skin_eQTL
rs12126004	HORMAD1	cis	Skin Sun Exposed Lower leg	GTEx
rs12126004	RP11-316M1.12	cis	Thyroid	GTEx
rs12126004	RP11-316M1.12	cis	Muscle Skeletal	GTEx
rs12126004	RP11-316M1.12	cis	Esophagus Muscularis	GTEx
rs12126004	HORMAD1	cis	Esophagus Mucosa	GTEx
rs12126004	CTSK	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:150879200-150898200	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr1:150887800-150890400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr1:150888000-150894800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin

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