Variant report

Variant	rs2688638
Chromosome Location	chr3:119321563-119321564
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 56 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10433338	0.96[ASN][1000 genomes]
rs13443	0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1525838	0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1534154	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];0.83[JPT][hapmap];0.87[TSI][hapmap];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1723969	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1797831	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1797832	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2049501	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2171025	0.83[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2248483	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2251566	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.91[TSI][hapmap];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2272267	0.96[ASN][1000 genomes]
rs2272268	0.96[ASN][1000 genomes]
rs2272269	0.96[ASN][1000 genomes]
rs2272270	0.96[ASN][1000 genomes]
rs2629399	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2629400	0.96[ASN][1000 genomes]
rs2629408	0.96[ASN][1000 genomes]
rs2670293	0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2670298	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2688637	0.94[ASW][hapmap];0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.86[MEX][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2688639	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2688646	0.96[ASN][1000 genomes]
rs2688647	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.91[TSI][hapmap];0.96[ASN][1000 genomes]
rs2688648	0.96[ASN][1000 genomes]
rs2692612	0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2692613	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2692614	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2692615	0.96[ASN][1000 genomes]
rs2692621	0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2692623	0.96[AFR][1000 genomes];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs474926	0.96[ASN][1000 genomes]
rs485257	1.00[ASN][1000 genomes]
rs487124	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs528765	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[JPT][hapmap];0.91[TSI][hapmap];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs530389	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs530783	0.83[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs536624	0.94[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs538136	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs551885	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs555525	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55670246	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55801535	0.87[ASN][1000 genomes]
rs56197198	0.81[ASN][1000 genomes]
rs58020513	0.94[ASN][1000 genomes]
rs593968	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs666134	0.94[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];0.80[MEX][hapmap];0.95[TSI][hapmap];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6807201	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6807613	0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72954966	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]

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	esv3487859	chr3:118570588-119419623	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
2	esv3487860	chr3:118570588-119419623	Strong transcription Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
3	nsv829695	chr3:119178890-119367996	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
4	esv1831824	chr3:119263607-119402474	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
5	nsv3963	chr3:119301064-119345904	Enhancers Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
6	nsv591363	chr3:119316828-119345950	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2688638	SLC12A8	cis	parietal	SCAN

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:119316200-119340600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr3:119317000-119323800	Weak transcription	HSMMtube	muscle
3	chr3:119317600-119327800	Weak transcription	Fetal Intestine Small	intestine
4	chr3:119318400-119321600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr3:119318400-119321600	Weak transcription	Gastric	stomach
6	chr3:119318400-119321800	Weak transcription	Pancreas	Pancrea
7	chr3:119318600-119344200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr3:119318800-119327800	Weak transcription	Liver	Liver
9	chr3:119319000-119321600	Weak transcription	Adipose Nuclei	Adipose
10	chr3:119319600-119321800	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr3:119319800-119321800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr3:119320000-119321600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr3:119320000-119321600	Weak transcription	HUES6 Cell Line	embryonic stem cell
14	chr3:119320000-119321600	Weak transcription	Skeletal Muscle Female	skeletal muscle
15	chr3:119320000-119321800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr3:119320000-119325600	Weak transcription	Spleen	Spleen
17	chr3:119320200-119321600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
18	chr3:119320200-119321600	Weak transcription	Left Ventricle	heart
19	chr3:119320200-119321800	Weak transcription	Placenta	Placenta
20	chr3:119320200-119321800	Weak transcription	Right Atrium	heart
21	chr3:119320200-119324000	Weak transcription	Lung	lung
22	chr3:119320200-119327400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr3:119320200-119345000	Weak transcription	Right Ventricle	heart
24	chr3:119320400-119321600	Weak transcription	Fetal Lung	lung
25	chr3:119321000-119322000	Flanking Active TSS	GM12878-XiMat	blood
26	chr3:119321200-119322000	Enhancers	HUVEC	blood vessel
27	chr3:119321400-119322000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin

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