Variant report

Variant	rs9831162
Chromosome Location	chr3:142813964-142813965
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:142805683..142809398-chr3:142813217..142818159,4	K562	blood:

Extended variants
information (count: 79 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs10413	0.84[EUR][1000 genomes]
rs1043898	1.00[CEU][hapmap];0.84[CHB][hapmap];0.91[GIH][hapmap];0.80[JPT][hapmap];0.82[TSI][hapmap];0.84[EUR][1000 genomes]
rs10451867	0.82[EUR][1000 genomes]
rs10513184	0.96[CEU][hapmap];0.91[GIH][hapmap];0.82[TSI][hapmap];0.82[EUR][1000 genomes]
rs1053950	1.00[CEU][hapmap];0.90[CHB][hapmap];0.91[GIH][hapmap];0.80[JPT][hapmap];0.82[TSI][hapmap];0.84[EUR][1000 genomes]
rs10790	0.89[CEU][hapmap];0.90[CHB][hapmap];0.80[JPT][hapmap];0.82[TSI][hapmap]
rs10935475	1.00[CEU][hapmap];0.84[CHB][hapmap];0.83[CHD][hapmap];0.91[GIH][hapmap]
rs10935479	0.84[EUR][1000 genomes]
rs11709036	0.96[CEU][hapmap];0.90[CHB][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12490776	0.82[EUR][1000 genomes]
rs12492904	1.00[CEU][hapmap]
rs13075955	0.82[EUR][1000 genomes]
rs13094293	1.00[CEU][hapmap];0.85[CHB][hapmap];0.91[GIH][hapmap];0.80[JPT][hapmap];0.84[TSI][hapmap];0.84[EUR][1000 genomes]
rs1349262	1.00[CEU][hapmap];0.90[CHB][hapmap];0.80[JPT][hapmap];0.84[EUR][1000 genomes]
rs13715	0.96[CEU][hapmap];0.81[EUR][1000 genomes]
rs1449868	1.00[CEU][hapmap];0.90[CHB][hapmap];0.91[GIH][hapmap];0.80[JPT][hapmap];0.82[TSI][hapmap];0.81[EUR][1000 genomes]
rs1449869	1.00[CEU][hapmap];0.90[CHB][hapmap];0.91[GIH][hapmap];0.80[JPT][hapmap];0.82[TSI][hapmap];0.84[EUR][1000 genomes]
rs1530753	1.00[CEU][hapmap];0.90[CHB][hapmap];0.80[JPT][hapmap];0.84[EUR][1000 genomes]
rs1532588	1.00[CEU][hapmap];0.90[CHB][hapmap];0.80[JPT][hapmap]
rs1814565	0.96[CEU][hapmap];0.91[GIH][hapmap]
rs1827159	1.00[CEU][hapmap];0.90[CHB][hapmap];0.80[JPT][hapmap];0.84[EUR][1000 genomes]
rs1839406	1.00[CEU][hapmap];0.90[CHB][hapmap];0.80[JPT][hapmap];0.81[EUR][1000 genomes]
rs1868569	0.84[EUR][1000 genomes]
rs1868570	0.84[EUR][1000 genomes]
rs1965343	1.00[CEU][hapmap];0.90[CHB][hapmap];0.80[JPT][hapmap]
rs2045306	0.84[EUR][1000 genomes]
rs2124541	1.00[CEU][hapmap];0.90[CHB][hapmap];0.83[CHD][hapmap];0.89[GIH][hapmap];0.80[JPT][hapmap];0.82[TSI][hapmap]
rs2124543	1.00[CEU][hapmap];0.84[CHB][hapmap]
rs2137586	0.96[CEU][hapmap]
rs2175739	0.96[CEU][hapmap]
rs2290549	0.89[CEU][hapmap];0.90[CHB][hapmap];0.80[JPT][hapmap]
rs2353408	0.84[EUR][1000 genomes]
rs2353409	0.84[EUR][1000 genomes]
rs2353411	1.00[CEU][hapmap];0.90[CHB][hapmap];0.88[GIH][hapmap];0.80[JPT][hapmap];0.82[TSI][hapmap];0.84[EUR][1000 genomes]
rs3821645	1.00[CEU][hapmap];0.90[CHB][hapmap];0.80[JPT][hapmap];0.84[EUR][1000 genomes]
rs3856697	1.00[CEU][hapmap];0.85[CHB][hapmap];0.91[GIH][hapmap];0.80[JPT][hapmap];0.84[TSI][hapmap];0.84[EUR][1000 genomes]
rs3902877	1.00[CEU][hapmap];0.89[CHB][hapmap];0.80[JPT][hapmap]
rs4030582	1.00[CEU][hapmap];0.90[CHB][hapmap];0.80[JPT][hapmap]
rs4683444	0.83[EUR][1000 genomes]
rs4683722	1.00[CEU][hapmap];0.83[CHB][hapmap];0.81[EUR][1000 genomes]
rs4683724	0.84[EUR][1000 genomes]
rs4683730	0.81[EUR][1000 genomes]
rs6440129	1.00[CEU][hapmap];0.90[CHB][hapmap];0.80[JPT][hapmap]
rs6440131	0.83[EUR][1000 genomes]
rs6440132	0.82[EUR][1000 genomes]
rs6440134	1.00[CEU][hapmap];0.89[CHB][hapmap];0.80[JPT][hapmap];0.84[EUR][1000 genomes]
rs6781080	0.81[EUR][1000 genomes]
rs6781887	1.00[CEU][hapmap];0.90[CHB][hapmap];0.80[JPT][hapmap]
rs6783145	0.81[EUR][1000 genomes]
rs6784200	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6805417	1.00[CEU][hapmap];0.90[CHB][hapmap];0.91[GIH][hapmap];0.80[JPT][hapmap];0.82[TSI][hapmap];0.83[EUR][1000 genomes]
rs6806551	0.82[EUR][1000 genomes]
rs6808406	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6808689	1.00[CEU][hapmap];0.90[CHB][hapmap];0.80[JPT][hapmap];0.81[EUR][1000 genomes]
rs7611721	1.00[CEU][hapmap];0.90[CHB][hapmap];0.91[GIH][hapmap];0.80[JPT][hapmap];0.82[TSI][hapmap];0.81[EUR][1000 genomes]
rs7623532	0.84[EUR][1000 genomes]
rs7648143	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs7649225	0.81[EUR][1000 genomes]
rs7652745	0.89[CEU][hapmap];0.90[CHB][hapmap];0.80[JPT][hapmap]
rs766360	0.96[CEU][hapmap];0.91[GIH][hapmap]
rs936194	0.84[EUR][1000 genomes]
rs936196	0.82[EUR][1000 genomes]
rs936197	0.82[EUR][1000 genomes]
rs937498	1.00[CEU][hapmap];0.85[CHB][hapmap];0.80[JPT][hapmap];0.84[EUR][1000 genomes]
rs9814656	0.96[CEU][hapmap];0.90[CHB][hapmap];0.85[EUR][1000 genomes]
rs9816317	0.84[EUR][1000 genomes]
rs9820175	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9835348	1.00[CEU][hapmap];0.85[CHB][hapmap];0.91[GIH][hapmap];0.80[JPT][hapmap];0.82[TSI][hapmap];0.81[EUR][1000 genomes]
rs9847059	0.85[EUR][1000 genomes]
rs9851353	0.84[EUR][1000 genomes]
rs9862433	0.84[EUR][1000 genomes]
rs9875210	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9877128	0.83[EUR][1000 genomes]
rs9877135	0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv877562	chr3:142573789-142846370	Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Enhancers Weak transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	esv2757893	chr3:142720230-142962932	Enhancers Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	esv2759183	chr3:142720230-142964373	Strong transcription Weak transcription Enhancers Bivalent Enhancer Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
4	nsv591921	chr3:142762487-142841740	Bivalent/Poised TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
5	nsv949288	chr3:142793323-143585882	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs9831162	SLC9A9	cis	parietal	SCAN
rs9831162	SR140	Cis_1M	lymphoblastoid	RTeQTL
rs9831162	U2SURP	cis	lymphoblastoid	seeQTL

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:142809600-142814000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr3:142812800-142814200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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