Variant report

Variant	rs12039443
Chromosome Location	chr1:169172290-169172291
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:169171835..169174311-chr1:169174995..169177628,2	MCF-7	breast:

Extended variants
information (count: 43 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10158265	1.00[ASN][1000 genomes]
rs10158861	0.97[ASN][1000 genomes]
rs10919102	1.00[ASN][1000 genomes]
rs10919146	0.97[ASN][1000 genomes]
rs11800843	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11808274	0.88[JPT][hapmap];0.82[ASN][1000 genomes]
rs11809378	0.87[ASN][1000 genomes]
rs12025233	1.00[ASN][1000 genomes]
rs12026996	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs12029853	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs12030320	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12032783	0.93[ASN][1000 genomes]
rs12033078	0.97[ASN][1000 genomes]
rs12033253	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12035804	0.82[ASN][1000 genomes]
rs12037211	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12038609	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs12040813	0.82[ASN][1000 genomes]
rs12043489	1.00[CHB][hapmap];0.88[JPT][hapmap];0.97[ASN][1000 genomes]
rs12043545	0.97[ASN][1000 genomes]
rs12046139	0.88[JPT][hapmap];0.97[ASN][1000 genomes]
rs12047231	1.00[ASN][1000 genomes]
rs1400838	0.89[JPT][hapmap]
rs1415928	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs1589113	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs16828170	0.88[JPT][hapmap];0.82[ASN][1000 genomes]
rs2268048	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs34710865	0.88[ASN][1000 genomes]
rs3766089	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs3820058	1.00[ASN][1000 genomes]
rs61806986	0.97[ASN][1000 genomes]
rs61808865	1.00[ASN][1000 genomes]
rs61808901	0.82[ASN][1000 genomes]
rs61808903	0.81[ASN][1000 genomes]
rs61808914	0.97[ASN][1000 genomes]
rs61808915	0.97[ASN][1000 genomes]
rs6685556	1.00[ASN][1000 genomes]
rs6698149	0.95[ASN][1000 genomes]
rs7521338	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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	nsv831858	chr1:169022383-169179068	Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
4	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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12039443	NME7	cis	Esophagus Muscularis	GTEx
rs12039443	NME7	cis	Artery Tibial	GTEx
rs12039443	NME7	Cis_1M	lymphoblastoid	RTeQTL
rs12039443	NME7	cis	Thyroid	GTEx

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:169130400-169195200	Weak transcription	Pancreas	Pancrea
2	chr1:169163600-169184000	Weak transcription	Ovary	ovary
3	chr1:169167200-169176400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
4	chr1:169167800-169186800	Weak transcription	Primary T cells from cord blood	blood
5	chr1:169168000-169183800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr1:169169600-169172600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr1:169169600-169175600	Weak transcription	Brain Anterior Caudate	brain
8	chr1:169169800-169172800	Enhancers	NHEK	skin
9	chr1:169169800-169173200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr1:169170000-169172600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr1:169170000-169172800	Enhancers	HMEC	breast
12	chr1:169170000-169175000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
13	chr1:169170200-169175000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr1:169171000-169173200	Weak transcription	NHLF	lung
15	chr1:169171600-169184000	Weak transcription	Fetal Intestine Small	intestine
16	chr1:169172000-169172400	Enhancers	Brain Germinal Matrix	brain
17	chr1:169172000-169174000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr1:169172000-169176600	Weak transcription	Colon Smooth Muscle	Colon
19	chr1:169172200-169172400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr1:169172200-169172400	Enhancers	Esophagus	oesophagus
21	chr1:169172200-169172400	Enhancers	Gastric	stomach
22	chr1:169172200-169173400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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