Variant report

Variant	rs13099253
Chromosome Location	chr3:67712970-67712971
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 70 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs11707967	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11712921	0.85[EUR][1000 genomes]
rs11717561	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11719952	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12714500	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13065696	1.00[CEU][hapmap];0.93[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.97[TSI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13068759	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13068996	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13069212	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13069251	1.00[CEU][hapmap];0.86[JPT][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13070332	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13076100	1.00[CEU][hapmap];0.86[CHB][hapmap];0.93[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13077262	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13081838	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13083820	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13086260	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13090197	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13091275	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13091330	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13092662	0.96[CEU][hapmap];0.82[CHB][hapmap];0.92[CHD][hapmap];0.83[GIH][hapmap];0.80[JPT][hapmap];0.94[MEX][hapmap];0.92[TSI][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1376028	1.00[CEU][hapmap];0.93[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.87[JPT][hapmap];0.87[MEX][hapmap];0.97[TSI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1376029	1.00[CEU][hapmap];0.82[CHB][hapmap];0.92[CHD][hapmap];0.83[GIH][hapmap];0.80[JPT][hapmap];0.87[MEX][hapmap];0.92[TSI][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1376030	1.00[CEU][hapmap];0.86[MEX][hapmap];0.92[TSI][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1450345	0.90[EUR][1000 genomes]
rs1473351	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1814519	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1823476	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2167181	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2198015	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2198016	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2218796	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2362453	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2362455	1.00[CEU][hapmap];0.87[CHB][hapmap];0.93[JPT][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62256429	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6766403	1.00[CEU][hapmap];0.93[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.87[JPT][hapmap];0.86[MEX][hapmap];0.97[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6774971	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6778266	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6779395	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6786211	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6787200	1.00[CEU][hapmap];0.93[CHB][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6787642	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6787853	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6788874	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6790771	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6791337	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6793868	1.00[CEU][hapmap];0.87[CHB][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];0.80[JPT][hapmap];0.87[MEX][hapmap];0.92[TSI][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6797010	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6797460	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6798228	1.00[CEU][hapmap];0.87[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];0.80[JPT][hapmap];0.83[LWK][hapmap];0.86[MEX][hapmap];0.95[TSI][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6806285	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6806536	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6808106	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs71621318	0.84[EUR][1000 genomes]
rs7434004	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7610446	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7615766	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7632886	0.80[EUR][1000 genomes]
rs7639427	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7647518	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7653350	0.82[EUR][1000 genomes]
rs881948	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs881949	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs935734	1.00[CEU][hapmap];0.93[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.87[JPT][hapmap];0.86[MEX][hapmap];0.97[TSI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9811187	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[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	nsv470638	chr3:67367341-67814738	Weak transcription ZNF genes & repeats Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
2	nsv460700	chr3:67393629-67712970	Genic enhancers Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv590560	chr3:67393629-67712970	Weak transcription Flanking Bivalent TSS/Enh Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	esv3359258	chr3:67589615-67828274	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv876922	chr3:67635506-67755257	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	nsv428739	chr3:67656829-67730379	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer 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	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs13099253	LRIG1	cis	parietal	SCAN
rs13099253	SUCLG2	Cis_1M	lymphoblastoid	RTeQTL
rs13099253	RP11-81N13.1	cis	Thyroid	GTEx

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:67705600-67713000	Weak transcription	Small Intestine	intestine
2	chr3:67705600-67756200	Weak transcription	Aorta	Aorta
3	chr3:67705800-67776000	Weak transcription	Ovary	ovary
4	chr3:67706400-67715600	Weak transcription	Duodenum Smooth Muscle	Duodenum
5	chr3:67706400-67721000	Weak transcription	Left Ventricle	heart
6	chr3:67706800-67726600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
7	chr3:67706800-67727200	Weak transcription	A549	lung
8	chr3:67707200-67713000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
9	chr3:67711400-67713000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
10	chr3:67711400-67713000	Enhancers	Primary T helper cells PMA-I stimulated	--
11	chr3:67711400-67713600	Enhancers	Fetal Lung	lung
12	chr3:67711400-67714800	Enhancers	Primary T cells from cord blood	blood
13	chr3:67711400-67715200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
14	chr3:67711400-67716400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
15	chr3:67711400-67717400	Enhancers	Primary T helper cells fromperipheralblood	blood
16	chr3:67711600-67713000	Enhancers	Primary T helper naive cells from peripheral blood	blood
17	chr3:67712000-67713800	Enhancers	Primary T cells fromperipheralblood	blood
18	chr3:67712200-67714400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
19	chr3:67712200-67728400	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr3:67712400-67713000	Weak transcription	Spleen	Spleen
21	chr3:67712800-67713800	Enhancers	Primary B cells from peripheral blood	blood
22	chr3:67712800-67714200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
23	chr3:67712800-67714600	Enhancers	Primary T killer memory cells from peripheral blood	blood
24	chr3:67712800-67715000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
25	chr3:67712800-67715000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood

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