Variant report

Variant	rs2460983
Chromosome Location	chr8:119672134-119672135
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 38 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10108302	0.95[ASN][1000 genomes]
rs1568484	0.82[ASN][1000 genomes]
rs2460964	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs2460965	1.00[CHB][hapmap];0.96[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.91[TSI][hapmap];0.84[ASN][1000 genomes]
rs2460966	1.00[CHB][hapmap];0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs2460967	0.86[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs2460968	0.86[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.84[ASN][1000 genomes]
rs2460970	1.00[CHB][hapmap];0.96[CHD][hapmap];0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs2460971	0.82[ASN][1000 genomes]
rs2460972	1.00[CHB][hapmap];0.90[JPT][hapmap];0.91[ASN][1000 genomes]
rs2460973	0.88[ASN][1000 genomes]
rs2460975	0.96[ASN][1000 genomes]
rs2460976	0.96[ASN][1000 genomes]
rs2460979	0.96[ASN][1000 genomes]
rs2460982	0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2514576	0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2514591	1.00[CHB][hapmap];0.92[CHD][hapmap];0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs2514592	1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs2514593	0.83[ASN][1000 genomes]
rs2514594	1.00[CHB][hapmap];0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs2514596	0.82[ASN][1000 genomes]
rs2514600	0.96[ASN][1000 genomes]
rs2514608	0.96[ASN][1000 genomes]
rs2514609	0.96[ASN][1000 genomes]
rs2514610	0.96[ASN][1000 genomes]
rs2514611	0.99[ASN][1000 genomes]
rs2514612	0.99[ASN][1000 genomes]
rs3133404	0.94[ASN][1000 genomes]
rs62531943	0.91[ASN][1000 genomes]
rs880033	1.00[CHB][hapmap];0.96[CHD][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs880034	1.00[CHB][hapmap];0.96[CHD][hapmap];0.82[GIH][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv891413	chr8:119607281-119679668	Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
2	esv1814789	chr8:119627671-119672134	Weak transcription Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	nsv465786	chr8:119627671-119767165	Flanking Active TSS Weak transcription Active TSS Enhancers Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv612048	chr8:119627671-119767165	Flanking Active TSS Bivalent/Poised TSS Active TSS Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv465787	chr8:119641169-119726242	Enhancers Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv470231	chr8:119641169-119726242	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	nsv612049	chr8:119641169-119726242	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs2460983	SAMD12	cis	lymphoblastoid	seeQTL
rs2460983	Hs.453941	cis	multi-tissue	Pritchard
rs2460983	SAMD12	cis	Lymphoblastoid	GTEx
rs2460983		cis	Lymphoblastoid	GTEx
rs2460983	SAMD12	cis	multi-tissue	Pritchard
rs2460983	LOC377696	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:119670400-119674000	Weak transcription	NHDF-Ad	bronchial
2	chr8:119670600-119672200	Enhancers	Stomach Smooth Muscle	stomach

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