Variant report

Variant	rs12242928
Chromosome Location	chr10:112798033-112798034
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 53 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10082499	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10787286	1.00[ASW][hapmap];0.80[CEU][hapmap];1.00[GIH][hapmap];0.92[LWK][hapmap];0.86[MEX][hapmap];0.91[MKK][hapmap];0.94[TSI][hapmap];0.84[AFR][1000 genomes]
rs10787291	1.00[ASW][hapmap];0.90[CEU][hapmap];1.00[GIH][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.87[EUR][1000 genomes]
rs10787293	1.00[ASW][hapmap];1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10787299	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10885059	1.00[YRI][hapmap];0.84[EUR][1000 genomes]
rs10885060	0.81[EUR][1000 genomes]
rs10885061	0.87[EUR][1000 genomes]
rs10885064	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10885071	0.97[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10885073	0.84[AFR][1000 genomes]
rs10885075	0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs10885076	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];0.85[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11195381	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11195387	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11195390	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.92[AFR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11195391	0.84[AFR][1000 genomes]
rs11195398	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12240685	0.83[EUR][1000 genomes]
rs12242177	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12246561	0.87[ASW][hapmap];0.85[CHB][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes]
rs12249031	0.92[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs12253351	0.84[AFR][1000 genomes]
rs12261765	0.87[EUR][1000 genomes]
rs12776359	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12776861	0.80[EUR][1000 genomes]
rs1571239	0.82[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs17186196	0.86[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs2146544	1.00[GIH][hapmap];0.84[LWK][hapmap];0.82[YRI][hapmap]
rs34401279	0.81[AFR][1000 genomes]
rs34893229	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35394459	0.81[AFR][1000 genomes]
rs35793075	0.86[EUR][1000 genomes]
rs35946882	0.81[AFR][1000 genomes]
rs3750619	0.87[ASW][hapmap];0.90[CEU][hapmap];1.00[GIH][hapmap];0.92[LWK][hapmap];0.86[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs3763692	0.81[AFR][1000 genomes]
rs61864641	0.86[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs6421360	1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs6585026	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7070962	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs7074629	0.92[AFR][1000 genomes]
rs7074653	0.81[AFR][1000 genomes]
rs7075507	0.93[ASN][1000 genomes]
rs7089069	0.81[AFR][1000 genomes]
rs7089193	0.82[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs7089615	0.87[ASN][1000 genomes]
rs7089687	1.00[ASW][hapmap];0.80[CEU][hapmap];0.88[TSI][hapmap];0.82[YRI][hapmap];0.84[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs7096359	0.87[ASW][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.94[MKK][hapmap];0.82[YRI][hapmap];0.92[AFR][1000 genomes]
rs7919142	1.00[GIH][hapmap]
rs7922142	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs9663346	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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	nsv831985	chr10:112652089-112803103	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12242928	LOC92482	Cis_1M	lymphoblastoid	RTeQTL
rs12242928	HABP2	cis	parietal	SCAN

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:112770800-112798800	Weak transcription	HMEC	breast
2	chr10:112783400-112801400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr10:112792800-112800400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr10:112797600-112798400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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