Variant report

Variant	rs10175972
Chromosome Location	chr2:47730521-47730522
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 58 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10175959	0.83[ASN][1000 genomes]
rs10179452	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10185866	0.92[CEU][hapmap];0.83[MEX][hapmap];0.83[TSI][hapmap]
rs10188090	0.85[ASN][1000 genomes]
rs10197011	0.81[ASN][1000 genomes]
rs10206575	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10206782	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10209369	0.81[CHB][hapmap]
rs10495945	0.80[CHB][hapmap];0.82[ASN][1000 genomes]
rs11684661	0.85[ASN][1000 genomes]
rs11684737	0.85[ASN][1000 genomes]
rs11886591	0.94[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs11901645	0.94[ASN][1000 genomes]
rs12712994	0.98[ASN][1000 genomes]
rs12991125	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13031342	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1981928	0.92[EUR][1000 genomes]
rs2059520	0.84[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs2303424	0.86[ASN][1000 genomes]
rs3732182	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3732183	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3764959	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3764960	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3771274	0.86[CHB][hapmap];0.95[JPT][hapmap]
rs3771278	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3771279	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3771280	0.90[CHB][hapmap];0.84[CHD][hapmap];0.90[JPT][hapmap];0.85[TSI][hapmap];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3771281	0.82[ASN][1000 genomes]
rs3821227	0.84[ASN][1000 genomes]
rs4550716	0.81[CHB][hapmap]
rs4583514	1.00[CHB][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs6544990	0.90[CHB][hapmap];0.90[JPT][hapmap]
rs6544992	0.89[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.92[CHD][hapmap];0.83[GIH][hapmap];0.81[JPT][hapmap];0.88[MEX][hapmap];0.94[TSI][hapmap];0.82[YRI][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6711675	0.86[CHB][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs6718364	0.85[ASN][1000 genomes]
rs6720549	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6725042	0.87[EUR][1000 genomes]
rs6726691	0.91[EUR][1000 genomes]
rs6737303	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6746426	0.85[ASN][1000 genomes]
rs6748435	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6757035	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6759990	0.81[CHB][hapmap];0.82[ASN][1000 genomes]
rs7565513	0.81[ASN][1000 genomes]
rs7584256	0.87[CEU][hapmap];0.85[TSI][hapmap]
rs7585174	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7588420	0.82[EUR][1000 genomes]
rs7596629	0.82[ASN][1000 genomes]
rs7599880	0.97[ASN][1000 genomes]
rs7607076	0.90[EUR][1000 genomes]
rs876936	0.85[CHB][hapmap];0.90[JPT][hapmap];0.86[ASN][1000 genomes]
rs876937	0.86[ASN][1000 genomes]
rs879722	0.85[ASN][1000 genomes]
rs9784092	0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1004828	chr2:47056849-47814482	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	144 gene(s)	inside rSNPs	diseases
2	nsv531348	chr2:47433147-47827310	Flanking Bivalent TSS/Enh Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
3	nsv999576	chr2:47506116-47773960	Weak transcription Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
4	nsv998314	chr2:47720420-47959168	Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Genic enhancers	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
rs10175972	MSH2	cis	Artery Tibial	GTEx
rs10175972	MSH2	cis	lung	GTEx

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:47727800-47731800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr2:47727800-47732200	Weak transcription	Primary T cells from cord blood	blood
3	chr2:47729600-47732000	Enhancers	Primary B cells from peripheral blood	blood
4	chr2:47729800-47731800	Flanking Active TSS	GM12878-XiMat	blood
5	chr2:47729800-47733800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr2:47730000-47731600	Enhancers	Primary B cells from cord blood	blood
7	chr2:47730000-47731800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
8	chr2:47730200-47730600	Enhancers	NHDF-Ad	bronchial
9	chr2:47730400-47730600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr2:47730400-47730600	Bivalent/Poised TSS	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr2:47730400-47735600	Weak transcription	HUVEC	blood vessel

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