Variant report

Variant	rs17024477
Chromosome Location	chr2:101140213-101140214
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 38 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10164820	0.82[CHB][hapmap]
rs10175632	0.95[CHB][hapmap]
rs10180172	0.87[CHB][hapmap]
rs10195943	0.91[CHB][hapmap]
rs10210508	0.90[CHB][hapmap]
rs11884976	0.91[CHB][hapmap];0.81[JPT][hapmap]
rs11891670	0.83[CHB][hapmap]
rs11898188	0.90[CHB][hapmap]
rs12233152	0.91[ASN][1000 genomes]
rs12464855	0.83[CHB][hapmap]
rs13408862	0.86[CHB][hapmap]
rs13415591	0.95[CHB][hapmap]
rs13419419	0.87[ASN][1000 genomes]
rs13421353	0.95[ASN][1000 genomes]
rs1437968	0.81[CEU][hapmap];0.95[CHB][hapmap];0.85[GIH][hapmap];0.92[MEX][hapmap];0.81[TSI][hapmap]
rs1437974	0.95[CHB][hapmap]
rs17024489	0.93[ASN][1000 genomes]
rs2309861	0.95[CHB][hapmap]
rs2309863	0.95[CHB][hapmap]
rs2871350	0.93[ASN][1000 genomes]
rs2871352	0.82[CHB][hapmap]
rs4147028	0.93[ASN][1000 genomes]
rs6542965	0.91[CHB][hapmap];0.81[JPT][hapmap]
rs6542966	0.81[ASN][1000 genomes]
rs6718127	0.81[ASN][1000 genomes]
rs6722896	0.91[CHB][hapmap];0.81[JPT][hapmap]
rs6732569	0.82[CHB][hapmap]
rs6739721	0.89[ASN][1000 genomes]
rs6755846	0.95[CHB][hapmap]
rs7595834	0.85[ASN][1000 genomes]
rs9308837	0.94[ASN][1000 genomes]
rs9653443	0.95[CHB][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:7)

SNP	Gene	Cis/trans	Tissue	Source
rs17024477	CHST10	cis	parietal	SCAN
rs17024477	MGAT4A	cis	parietal	SCAN
rs17024477	AFF3	cis	cerebellum	SCAN
rs17024477	AFF3	cis	parietal	SCAN
rs17024477	ANKRD36B	cis	parietal	SCAN
rs17024477	LYG2	cis	parietal	SCAN
rs17024477	COX5B	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:101136800-101149000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr2:101140000-101140400	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr2:101140000-101141000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin

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