Variant report

Variant	rs11602909
Chromosome Location	chr11:34768003-34768004
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 117 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:101)

rs_ID	r²[population]
rs10501134	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10501136	1.00[JPT][hapmap]
rs11032804	0.88[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs11032806	0.80[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs11600402	0.84[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs11601205	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11601422	0.84[ASN][1000 genomes]
rs11601923	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11602318	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11602669	0.84[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs11602944	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11603718	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11603774	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11604069	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11604882	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11605785	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11607035	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11607300	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11819839	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11821793	0.80[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs12278295	1.00[JPT][hapmap]
rs12291580	1.00[JPT][hapmap]
rs1258464	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1258466	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1258468	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1258469	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1258470	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12792532	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12800220	0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs12801509	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12802120	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12802323	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12802798	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12803316	0.83[ASN][1000 genomes]
rs12809046	0.86[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs1355221	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1355222	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1355223	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1361645	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1377495	0.88[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs1396879	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1396883	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1453380	0.85[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs1453387	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1539250	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1539251	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1578622	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1588353	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1597962	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1703996	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17293467	1.00[CHB][hapmap];0.93[JPT][hapmap];0.83[ASN][1000 genomes]
rs17359064	1.00[CHB][hapmap];0.93[JPT][hapmap]
rs1773908	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1773910	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1869360	0.80[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs1901831	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2185700	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2221720	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2226113	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2281908	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs286858	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs286861	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs286862	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs286864	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs286885	0.89[ASN][1000 genomes]
rs286893	1.00[CHB][hapmap];0.93[JPT][hapmap];0.82[ASN][1000 genomes]
rs34282125	0.80[ASN][1000 genomes]
rs34284115	0.83[ASN][1000 genomes]
rs34610590	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34729653	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34751755	0.84[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs34875830	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35032224	0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs35357012	0.84[ASN][1000 genomes]
rs3818514	0.88[CEU][hapmap];0.92[CHB][hapmap];0.93[JPT][hapmap];0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs4465347	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs448016	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs5010670	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60130036	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61881050	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6484726	0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs680727	0.91[ASN][1000 genomes]
rs704744	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7101790	0.86[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs7102625	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7112608	0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs7116409	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7121272	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7129089	0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs7130325	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7925421	0.88[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.80[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs7943363	0.84[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs7943755	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs7944030	0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs836462	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs836466	0.92[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs836467	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs860712	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs865070	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs896856	1.00[CHB][hapmap];0.93[JPT][hapmap];0.83[ASN][1000 genomes]
rs913204	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832117	chr11:34639008-34831199	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
2	nsv1045130	chr11:34641598-34777725	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
3	nsv1052192	chr11:34641598-34781288	ZNF genes & repeats Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
4	nsv1051492	chr11:34641598-34789331	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
5	nsv1052008	chr11:34641598-34794024	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
6	nsv467788	chr11:34642493-34770494	Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
7	nsv553998	chr11:34642493-34770494	Enhancers Strong transcription Active TSS ZNF genes & repeats Weak transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
8	nsv518807	chr11:34642493-34780936	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
9	nsv519718	chr11:34642493-34780936	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
10	nsv467789	chr11:34642493-34780936	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
11	nsv467790	chr11:34642493-34780936	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
12	nsv553999	chr11:34642493-34780936	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
13	nsv554000	chr11:34643780-34780936	Genic enhancers Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
14	nsv869812	chr11:34648088-34810956	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
15	nsv832118	chr11:34743123-34903951	Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
16	nsv897214	chr11:34764251-34821948	Weak transcription Bivalent Enhancer Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	n/a

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs11602909	APIP	cis	Thyroid	GTEx
rs11602909	APIP	cis	Esophagus Muscularis	GTEx
rs11602909	APIP	cis	Artery Aorta	GTEx
rs11602909	APIP	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:34752800-34770800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr11:34759800-34780000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr11:34760200-34774400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr11:34760200-34776200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr11:34760200-34776800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr11:34760400-34787000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr11:34762200-34776000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
8	chr11:34764800-34776200	Weak transcription	HUES64 Cell Line	embryonic stem cell
9	chr11:34765000-34777000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr11:34765200-34787000	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr11:34767000-34769600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr11:34767000-34770000	Weak transcription	Psoas Muscle	Psoas
13	chr11:34767000-34770800	Weak transcription	Pancreas	Pancrea
14	chr11:34767400-34768400	Weak transcription	Duodenum Mucosa	Duodenum
15	chr11:34767400-34769600	Weak transcription	Placenta	Placenta
16	chr11:34767400-34769800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
17	chr11:34767400-34770200	Weak transcription	Gastric	stomach

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