Variant report

Variant	rs2514594
Chromosome Location	chr8:119625149-119625150
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 32 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10108302	0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1568484	0.98[ASN][1000 genomes]
rs2460964	1.00[CHB][hapmap];0.91[JPT][hapmap];0.96[ASN][1000 genomes]
rs2460965	0.93[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2460966	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2460967	0.86[CEU][hapmap];0.93[CHB][hapmap];0.91[JPT][hapmap];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2460968	0.86[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2460970	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2460971	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2460972	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2460975	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2460976	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2460979	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2460982	0.83[ASN][1000 genomes]
rs2460983	0.82[ASN][1000 genomes]
rs2514576	0.83[ASN][1000 genomes]
rs2514591	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2514592	1.00[CHB][hapmap];0.90[JPT][hapmap];0.96[ASN][1000 genomes]
rs2514593	0.96[ASN][1000 genomes]
rs2514596	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2514600	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2514608	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2514609	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2514610	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2514611	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2514612	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3133404	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62531943	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs880033	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs880034	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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	esv3429273	chr8:119625038-119625199	Weak transcription	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs2514594	Hs.453941	cis	multi-tissue	Pritchard
rs2514594		cis	Lymphoblastoid	GTEx
rs2514594	LOC377696	cis	multi-tissue	Pritchard
rs2514594	SAMD12	cis	multi-tissue	Pritchard
rs2514594	SAMD12	cis	Skin Sun Exposed Lower leg	GTEx
rs2514594	SAMD12	cis	Lymphoblastoid	GTEx

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:119605800-119631800	Weak transcription	Fetal Intestine Small	intestine
2	chr8:119609200-119633000	Weak transcription	Gastric	stomach
3	chr8:119609400-119633600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr8:119610400-119626600	Weak transcription	Brain Anterior Caudate	brain
5	chr8:119614600-119626600	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr8:119619400-119632200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr8:119620600-119626600	Weak transcription	Left Ventricle	heart
8	chr8:119622200-119626400	Weak transcription	Brain Substantia Nigra	brain
9	chr8:119622200-119626600	Weak transcription	Lung	lung
10	chr8:119622200-119626600	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr8:119622200-119626800	Weak transcription	Brain Hippocampus Middle	brain
12	chr8:119622400-119626400	Weak transcription	Brain Angular Gyrus	brain
13	chr8:119622400-119627000	Weak transcription	NHEK	skin
14	chr8:119622800-119626400	Weak transcription	Right Atrium	heart
15	chr8:119622800-119626800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr8:119623000-119626200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr8:119623000-119626400	Weak transcription	Brain Cingulate Gyrus	brain
18	chr8:119623200-119626600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr8:119623200-119626600	Weak transcription	Right Ventricle	heart
20	chr8:119623200-119626800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
21	chr8:119623200-119627000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr8:119623200-119632200	Weak transcription	Pancreatic Islets	Pancreatic Islet
23	chr8:119623800-119632800	Weak transcription	Fetal Lung	lung
24	chr8:119624200-119632800	Weak transcription	Pancreas	Pancrea
25	chr8:119624400-119628600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
26	chr8:119625000-119625200	Weak transcription	GM12878-XiMat	blood

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