Variant report

Variant	rs1396883
Chromosome Location	chr11:34757447-34757448
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 117 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:102)

rs_ID	r²[population]
rs10501134	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10501136	0.85[CHD][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap]
rs11032804	0.88[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs11032806	0.80[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs11600402	0.84[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs11601205	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11601422	0.82[ASN][1000 genomes]
rs11601923	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11602318	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11602669	0.84[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs11602909	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11602944	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11603718	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11603774	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11604069	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11604882	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11605785	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11607035	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11607300	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11819839	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11821793	0.80[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs12278295	1.00[JPT][hapmap]
rs12291580	1.00[JPT][hapmap]
rs12417662	0.82[ASN][1000 genomes]
rs1258464	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1258466	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1258468	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1258469	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1258470	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12792532	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12800220	0.84[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs12801509	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12802120	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12802323	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12802798	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12803316	0.86[ASN][1000 genomes]
rs12809046	0.86[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs1355221	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1355222	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1355223	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1361645	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1377495	0.88[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.84[GIH][hapmap];0.94[JPT][hapmap];0.91[MEX][hapmap];0.88[TSI][hapmap];0.82[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs1396879	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1453380	0.85[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs1453387	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1539250	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1539251	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1578622	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1588353	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1597962	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1703996	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17293467	1.00[CHB][hapmap];0.94[JPT][hapmap];0.86[ASN][1000 genomes]
rs17359064	1.00[CHB][hapmap];0.94[JPT][hapmap];0.82[ASN][1000 genomes]
rs1773908	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1773910	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1869360	0.80[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs1901831	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2185700	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2221720	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2226113	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2281908	0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs286858	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs286861	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs286862	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs286864	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs286885	0.92[ASN][1000 genomes]
rs286893	1.00[CHB][hapmap];0.94[JPT][hapmap];0.85[ASN][1000 genomes]
rs34284115	0.86[ASN][1000 genomes]
rs34610590	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34729653	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34751755	0.84[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs34875830	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35032224	0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs35357012	0.82[ASN][1000 genomes]
rs3818514	0.88[CEU][hapmap];0.92[CHB][hapmap];0.92[CHD][hapmap];0.84[GIH][hapmap];0.94[JPT][hapmap];0.91[MEX][hapmap];0.88[TSI][hapmap];0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs4465347	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs448016	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs5010670	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs60130036	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61881050	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6484726	0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs680727	0.93[ASN][1000 genomes]
rs704744	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7101790	0.86[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs7102625	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7112608	0.83[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs7116409	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7121272	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7129089	0.83[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs7130325	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7131090	0.82[ASN][1000 genomes]
rs7925421	0.88[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.84[GIH][hapmap];0.94[JPT][hapmap];0.87[MEX][hapmap];0.88[TSI][hapmap];0.80[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs7943363	0.84[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs7943755	0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs7944030	0.83[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs836462	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs836466	0.92[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs836467	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs860712	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs865070	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs896856	1.00[CHB][hapmap];0.94[JPT][hapmap];0.86[ASN][1000 genomes]
rs913204	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 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

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs1396883	APIP	cis	Skin Sun Exposed Lower leg	GTEx
rs1396883	APIP	cis	multi-tissue	Pritchard
rs1396883	APIP	cis	Esophagus Muscularis	GTEx
rs1396883	APIP	cis	cerebellum	SCAN
rs1396883	PDHX	cis	cerebellum	SCAN

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:34731600-34758000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr11:34731600-34759200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr11:34735000-34761600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr11:34738200-34759400	Weak transcription	Placenta	Placenta
5	chr11:34752800-34770800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr11:34753000-34757800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
7	chr11:34753800-34757800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr11:34753800-34760400	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr11:34756600-34758800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr11:34756800-34758600	ZNF genes & repeats	iPS-18 Cell Line	embryonic stem cell
11	chr11:34756800-34759000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr11:34756800-34760000	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
13	chr11:34757200-34757600	Strong transcription	H1 Cell Line	embryonic stem cell
14	chr11:34757200-34757600	Strong transcription	H9 Cell Line	embryonic stem cell
15	chr11:34757200-34758000	Strong transcription	HUES6 Cell Line	embryonic stem cell
16	chr11:34757200-34760200	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived

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