Variant report

Variant	rs12046139
Chromosome Location	chr1:169308714-169308715
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 47 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10158265	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10158861	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10919088	0.82[AMR][1000 genomes]
rs10919102	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10919146	1.00[ASN][1000 genomes]
rs10919155	0.89[JPT][hapmap]
rs11800843	0.82[CHB][hapmap];0.88[JPT][hapmap]
rs11809378	0.90[ASN][1000 genomes]
rs12025233	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12026996	0.82[CHB][hapmap];0.88[JPT][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12029853	0.82[CHB][hapmap];0.86[JPT][hapmap];0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12030320	0.82[CHB][hapmap];0.89[JPT][hapmap]
rs12032783	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12033078	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12033253	0.82[CHB][hapmap];0.89[JPT][hapmap]
rs12037211	0.82[CHB][hapmap];0.88[JPT][hapmap];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12038609	0.82[CHB][hapmap];0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12039443	0.88[JPT][hapmap];0.97[ASN][1000 genomes]
rs12043489	0.82[CHB][hapmap];0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12043545	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12045202	0.82[AMR][1000 genomes]
rs12047231	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1415928	0.82[CHB][hapmap];0.88[JPT][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1589113	0.82[CHB][hapmap];0.86[JPT][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16862172	0.82[CHB][hapmap];0.88[JPT][hapmap]
rs2235195	0.82[CHB][hapmap];0.88[JPT][hapmap]
rs2268048	0.82[CHB][hapmap];0.88[JPT][hapmap];0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34710865	0.92[ASN][1000 genomes]
rs3766089	0.82[CHB][hapmap];0.88[JPT][hapmap];0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3820058	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56341747	0.82[AMR][1000 genomes]
rs61806986	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61808865	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61808914	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61808915	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6685556	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6698149	0.91[ASN][1000 genomes]
rs7521338	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9633334	0.82[AMR][1000 genomes]
rs9988604	0.82[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3522071	chr1:168978325-169339044	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
2	esv3522072	chr1:168978325-169339044	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' Weak transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
3	esv10418	chr1:169059628-169621268	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
4	nsv1010010	chr1:169189586-169347545	Active TSS Weak transcription Flanking Active TSS Genic enhancers Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv872531	chr1:169191860-169388193	Active TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	nsv1012919	chr1:169200982-169324750	Flanking Active TSS Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	nsv872532	chr1:169275630-169363203	Strong transcription Flanking Active TSS Enhancers Weak transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:169260400-169310400	Weak transcription	Fetal Stomach	stomach
2	chr1:169265000-169320400	Weak transcription	Aorta	Aorta
3	chr1:169270200-169336400	Weak transcription	Stomach Smooth Muscle	stomach
4	chr1:169273600-169312400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr1:169291000-169313200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr1:169296600-169310400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr1:169296600-169324600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr1:169303000-169312600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr1:169303800-169317600	Weak transcription	Liver	Liver
10	chr1:169304800-169313200	Weak transcription	Spleen	Spleen
11	chr1:169305400-169308800	Weak transcription	Ovary	ovary
12	chr1:169305600-169312400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
13	chr1:169305600-169336400	Weak transcription	Left Ventricle	heart
14	chr1:169306600-169309000	Enhancers	Primary hematopoietic stem cells short term culture	blood
15	chr1:169306600-169309200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr1:169306800-169309200	Enhancers	Primary hematopoietic stem cells	blood
17	chr1:169306800-169310400	Weak transcription	Fetal Intestine Large	intestine
18	chr1:169307000-169310400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr1:169307000-169310400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr1:169307600-169309000	Enhancers	Dnd41	blood
21	chr1:169307600-169309400	Enhancers	K562	blood
22	chr1:169308000-169311200	Weak transcription	Pancreatic Islets	Pancreatic Islet
23	chr1:169308200-169309400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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