Variant report

Variant	rs17024473
Chromosome Location	chr2:101139102-101139103
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 64 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs12614705	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap]
rs12619028	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12619423	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12620497	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12620836	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12621241	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12623984	0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17024288	0.91[EUR][1000 genomes]
rs17024415	0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17024421	0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17024434	0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17024457	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17024467	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17024471	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17024474	0.93[ASN][1000 genomes]
rs17024480	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55796343	0.91[EUR][1000 genomes]
rs55827030	0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs55849205	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56100007	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61620481	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61647034	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6542952	1.00[JPT][hapmap]
rs6705910	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs6709376	0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6709957	0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6716842	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs6730520	0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6738492	0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6745149	0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72821202	0.91[EUR][1000 genomes]
rs72823210	0.91[EUR][1000 genomes]
rs72823211	0.91[EUR][1000 genomes]
rs72823212	0.91[EUR][1000 genomes]
rs72823215	0.91[EUR][1000 genomes]
rs72823243	0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72823244	0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72823245	0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72823252	0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72823264	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72823265	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72823266	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72823268	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72823269	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72823271	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72823274	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72823277	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72825294	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72825295	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72825302	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7574649	0.91[EUR][1000 genomes]
rs7577785	0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7587950	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7597493	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7604140	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7604590	0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7608774	1.00[CEU][hapmap]
rs962556	1.00[CHD][hapmap];1.00[JPT][hapmap]

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	nsv1007777	chr2:100816913-101308914	Active TSS Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
2	nsv535844	chr2:100816913-101308914	Flanking Bivalent TSS/Enh Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
3	nsv582531	chr2:100908508-101207639	Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
4	nsv916792	chr2:101021066-101525200	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
5	nsv582532	chr2:101029002-101531943	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
6	nsv834312	chr2:101044438-101238166	Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs17024473	SLC47A2	trans	brain	seeQTL
rs17024473	CAPS	trans	brain	seeQTL
rs17024473	BOK	trans	brain	seeQTL

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:101135600-101140000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr2:101135600-101140000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr2:101136800-101149000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr2:101138600-101139600	Enhancers	Fetal Intestine Large	intestine
5	chr2:101138800-101139400	Enhancers	Duodenum Mucosa	Duodenum
6	chr2:101138800-101139400	Bivalent Enhancer	HepG2	liver

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