Variant report

Variant	rs11804170
Chromosome Location	chr1:169884743-169884744
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:169884029..169885791-chr1:169886642..169888521,2	MCF-7	breast:
2	chr1:169883530..169886106-chr1:169901752..169904376,3	K562	blood:
3	chr1:169861017..169866202-chr1:169878725..169885490,9	MCF-7	breast:

Variant related genes	Relation type
ENSG00000000457	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10159425	0.84[EUR][1000 genomes]
rs10489170	0.85[CEU][hapmap];0.82[CHB][hapmap];0.88[JPT][hapmap]
rs10489177	0.85[CEU][hapmap]
rs10800477	0.85[CEU][hapmap]
rs10800494	0.93[CEU][hapmap];0.90[CHB][hapmap]
rs10800495	0.93[CEU][hapmap];0.90[CHB][hapmap]
rs10919260	0.85[CEU][hapmap];0.82[CHB][hapmap];0.88[JPT][hapmap]
rs10919270	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10919271	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10919272	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10919284	0.90[CHB][hapmap];0.86[JPT][hapmap]
rs11803298	0.94[CEU][hapmap];0.90[CHB][hapmap]
rs11807267	0.85[ASN][1000 genomes]
rs12123693	0.93[CEU][hapmap];0.90[CHB][hapmap]
rs12124607	0.94[CEU][hapmap];0.90[CHB][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs12126204	0.94[CEU][hapmap];0.90[CHB][hapmap]
rs12128754	0.85[CEU][hapmap]
rs12137754	0.94[CEU][hapmap];0.90[CHB][hapmap];0.86[JPT][hapmap]
rs12138675	0.85[CEU][hapmap];0.82[CHB][hapmap];0.88[JPT][hapmap];0.81[AMR][1000 genomes]
rs12146137	0.93[CEU][hapmap];0.90[CHB][hapmap]
rs12401321	0.92[AFR][1000 genomes];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12401338	0.85[EUR][1000 genomes]
rs12750962	0.80[CHB][hapmap]
rs12754717	0.85[ASN][1000 genomes]
rs12757747	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12760433	0.87[CEU][hapmap]
rs1360293	0.94[CEU][hapmap];0.90[CHB][hapmap]
rs2273457	0.86[JPT][hapmap]
rs35275808	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs35414012	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35688996	0.83[CEU][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs6427229	0.87[CEU][hapmap];0.90[CHB][hapmap];0.86[JPT][hapmap];0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6427233	0.93[CEU][hapmap];0.90[CHB][hapmap]
rs6657512	0.93[CEU][hapmap];0.90[CHB][hapmap]
rs6670191	0.94[CEU][hapmap];0.90[CHB][hapmap]
rs6679646	0.85[CEU][hapmap];0.82[CHB][hapmap];0.84[AMR][1000 genomes]
rs6688806	0.86[CEU][hapmap];0.82[CHB][hapmap];0.88[JPT][hapmap]
rs682449	0.86[ASN][1000 genomes]
rs74122428	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7514634	0.94[CEU][hapmap];0.90[CHB][hapmap];0.85[JPT][hapmap];0.82[ASN][1000 genomes]
rs7521273	0.86[CEU][hapmap];0.85[JPT][hapmap]
rs7533194	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7540497	0.93[ASN][1000 genomes]
rs7552710	0.87[CEU][hapmap]
rs882595	0.85[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3451367	chr1:169630075-169976964	Strong transcription Flanking Active TSS Genic enhancers Enhancers Weak transcription Active TSS ZNF genes & repeats 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	37 gene(s)	inside rSNPs	diseases
2	esv1814601	chr1:169782006-169885186	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
3	esv1821503	chr1:169782006-169885186	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
4	esv1847722	chr1:169782006-169885186	Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
5	esv2757760	chr1:169782006-169885186	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
6	esv2758976	chr1:169782006-169885186	Strong transcription Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Enhancers Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
7	nsv428268	chr1:169782006-169885186	Strong transcription ZNF genes & repeats Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
8	esv1845220	chr1:169782006-169933886	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:169872800-169887800	Weak transcription	Primary T cells from cord blood	blood
2	chr1:169875800-169889800	Weak transcription	Fetal Brain Female	brain
3	chr1:169876200-169903600	Weak transcription	Aorta	Aorta
4	chr1:169877600-169889800	Weak transcription	Lung	lung
5	chr1:169878400-169892200	Weak transcription	Duodenum Mucosa	Duodenum
6	chr1:169878400-169895200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr1:169878400-169946200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
8	chr1:169878600-169895000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
9	chr1:169880200-169892800	Weak transcription	Fetal Heart	heart
10	chr1:169881000-169888000	Weak transcription	Fetal Brain Male	brain
11	chr1:169881400-169901000	Weak transcription	Skeletal Muscle Female	skeletal muscle
12	chr1:169882200-169892000	Weak transcription	Brain Germinal Matrix	brain
13	chr1:169882800-169886800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
14	chr1:169883000-169886800	Weak transcription	Fetal Stomach	stomach
15	chr1:169883000-169890600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
16	chr1:169883200-169885200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr1:169883800-169884800	Flanking Active TSS	GM12878-XiMat	blood
18	chr1:169884200-169913000	Weak transcription	Rectal Mucosa Donor 29	rectum
19	chr1:169884400-169885200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr1:169884400-169888200	Weak transcription	Adipose Nuclei	Adipose
21	chr1:169884400-169889000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr1:169884400-169891000	Weak transcription	Esophagus	oesophagus
23	chr1:169884600-169887600	Weak transcription	Fetal Muscle Trunk	muscle
24	chr1:169884600-169887800	Weak transcription	Small Intestine	intestine
25	chr1:169884600-169888400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr1:169884600-169888600	Weak transcription	NH-A	brain
27	chr1:169884600-169892800	Weak transcription	Pancreas	Pancrea
28	chr1:169884600-169895200	Weak transcription	Fetal Intestine Small	intestine
29	chr1:169884600-169900600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr1:169884600-169900600	Weak transcription	NHDF-Ad	bronchial

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