Variant report

Variant	rs17128356
Chromosome Location	chr10:112832225-112832226
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr10:112831915-112832403	H1-neurons	neurons:	n/a	n/a
2	POLR2A	chr10:112831783-112832418	H1-neurons	neurons:	n/a	n/a
3	NR3C1	chr10:112832016-112832294	A549	lung:	n/a	n/a

Variant related genes	Relation type
ADRA2A	TF binding region

Extended variants
information (count: 28 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs11195397	0.88[TSI][hapmap]
rs11195405	0.87[CEU][hapmap];0.95[JPT][hapmap];0.93[YRI][hapmap];0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11195417	0.82[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11195419	0.83[ASW][hapmap];0.88[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs11815669	0.94[ASN][1000 genomes]
rs12569835	0.91[EUR][1000 genomes]
rs12571756	0.86[CEU][hapmap];0.94[JPT][hapmap];0.86[YRI][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17128130	0.83[EUR][1000 genomes]
rs17128212	0.83[ASW][hapmap];0.87[CEU][hapmap];0.90[GIH][hapmap];0.95[JPT][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1800545	0.96[ASN][1000 genomes]
rs3750625	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.83[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs4391757	0.94[EUR][1000 genomes]
rs55794717	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs56233990	0.85[EUR][1000 genomes]
rs56784382	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs56909097	0.85[AFR][1000 genomes]
rs56946887	0.91[EUR][1000 genomes]
rs58018669	0.92[ASN][1000 genomes]
rs7072811	0.95[JPT][hapmap];0.88[EUR][1000 genomes]
rs7073594	0.91[ASW][hapmap];0.87[CEU][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap];0.92[LWK][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7073880	0.87[CEU][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs73343848	0.91[EUR][1000 genomes]
rs73343859	0.91[EUR][1000 genomes]
rs73343879	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs73345956	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7913823	0.82[AFR][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	nsv498045	chr10:112794518-113353550	Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv825566	chr10:112830014-112871333	Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17128356	SHOC2	cis	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:112829800-112835600	Weak transcription	Pancreas	Pancrea
2	chr10:112831400-112835600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr10:112831800-112832800	Enhancers	HSMM	muscle

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