Variant report

Variant	rs1258469
Chromosome Location	chr11:34729371-34729372
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr11:34729360-34729372	Gliobla	brain:	n/a	n/a
2	CTCF	chr11:34729240-34729390	HEEpiC	esophagus:	n/a	n/a

Variant related genes	Relation type
ENSG00000271369	TF binding region

Extended variants
information (count: 123 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:105)

rs_ID	r²[population]
rs10501134	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11032804	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11032806	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11600402	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11601205	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11601923	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11602318	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11602669	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11602909	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11602944	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11603718	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11603774	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11604069	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11604882	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11605785	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11607035	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11607300	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11819839	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11821793	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12417662	0.86[ASN][1000 genomes]
rs1258464	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1258466	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1258468	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1258470	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12788231	0.80[ASN][1000 genomes]
rs12792532	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12800220	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12801509	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12802120	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12802323	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12802798	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12803316	0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12809046	0.92[ASN][1000 genomes]
rs1355221	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1355222	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1355223	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1361645	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1377495	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1396879	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1396883	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1453380	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1453387	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1539250	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1539251	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1578622	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1588353	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1597960	0.88[AFR][1000 genomes]
rs1597961	0.88[AFR][1000 genomes]
rs1597962	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1703996	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17293467	0.89[ASN][1000 genomes]
rs17359064	0.86[ASN][1000 genomes]
rs1773908	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1773910	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1869360	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1901830	0.87[AFR][1000 genomes]
rs1901831	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2084970	0.87[AFR][1000 genomes]
rs2185700	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2221720	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2226113	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2281908	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs286858	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs286861	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs286862	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs286864	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs286885	0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs286893	0.88[ASN][1000 genomes]
rs34284115	0.81[ASN][1000 genomes]
rs34610590	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34729653	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34751755	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34875830	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35032224	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3818514	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4465347	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs448016	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs5010670	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs60130036	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61881050	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6484726	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs680727	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs704744	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7101790	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7102625	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7112608	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7116409	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7121272	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7125773	0.86[AFR][1000 genomes]
rs7127169	0.88[AFR][1000 genomes]
rs7129089	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7130325	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7131090	0.86[ASN][1000 genomes]
rs7925421	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7936076	0.83[AFR][1000 genomes]
rs7943363	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7943755	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7944030	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs836462	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs836466	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs836467	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs860712	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs865070	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs896856	0.89[ASN][1000 genomes]
rs913204	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:18 , 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	nsv897213	chr11:34695389-34752562	ZNF genes & repeats Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
16	esv3322562	chr11:34726276-34730574	Enhancers Weak transcription ZNF genes & repeats	TF binding region	1 gene(s)	inside rSNPs	n/a
17	nsv512218	chr11:34727381-34729414	Weak transcription Enhancers ZNF genes & repeats	TF binding region	1 gene(s)	inside rSNPs	n/a
18	esv3488216	chr11:34727426-34729624	Weak transcription Enhancers ZNF genes & repeats	TF binding region	1 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:34716800-34731000	Weak transcription	H1 Cell Line	embryonic stem cell
2	chr11:34724200-34730800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr11:34724200-34731000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr11:34724200-34731000	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr11:34724200-34731200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr11:34724200-34731200	Weak transcription	Placenta	Placenta
7	chr11:34724400-34733600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr11:34725000-34731000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
9	chr11:34725400-34730800	Weak transcription	HUES64 Cell Line	embryonic stem cell
10	chr11:34728200-34729600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
11	chr11:34728400-34729400	Enhancers	NHEK	skin
12	chr11:34728400-34729600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr11:34728400-34729600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
14	chr11:34728400-34729600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr11:34728400-34729600	Enhancers	Esophagus	oesophagus
16	chr11:34728600-34729400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr11:34728600-34729600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr11:34728800-34729800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr11:34728800-34730200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr11:34729000-34729600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr11:34729000-34729800	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr11:34729000-34730600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr11:34729200-34729400	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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