Variant report

Variant	rs61806242
Chromosome Location	chr1:169175465-169175466
allele	C/T
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: 91 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:87)

rs_ID	r²[population]
rs10442644	0.81[AMR][1000 genomes]
rs10800413	0.82[EUR][1000 genomes]
rs10800418	0.82[EUR][1000 genomes]
rs10919075	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10919099	0.82[EUR][1000 genomes]
rs10919101	0.82[EUR][1000 genomes]
rs11810319	0.83[EUR][1000 genomes]
rs12080100	0.82[EUR][1000 genomes]
rs12084793	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12116551	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12116683	0.81[EUR][1000 genomes]
rs12117362	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12117559	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12118611	0.81[EUR][1000 genomes]
rs12118645	0.81[EUR][1000 genomes]
rs12120007	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12120960	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12122348	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12124064	0.81[EUR][1000 genomes]
rs12124738	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12125057	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12129132	0.81[EUR][1000 genomes]
rs12130858	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12140995	0.82[EUR][1000 genomes]
rs12143790	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12143963	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12144230	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12144832	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12145193	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12145897	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12723917	0.81[EUR][1000 genomes]
rs12728614	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12730917	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12730920	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12736817	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12740501	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12741323	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12743588	0.81[EUR][1000 genomes]
rs12745978	0.81[EUR][1000 genomes]
rs12750161	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12751407	0.81[EUR][1000 genomes]
rs12751571	0.81[EUR][1000 genomes]
rs12753816	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs17345170	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17345184	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17349271	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17349439	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17349467	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1936533	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2040446	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2157597	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2179491	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs34248820	0.81[EUR][1000 genomes]
rs34408435	0.81[EUR][1000 genomes]
rs34829200	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs34975352	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs35091267	0.80[EUR][1000 genomes]
rs35133990	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs35220898	0.81[EUR][1000 genomes]
rs35271076	0.81[EUR][1000 genomes]
rs35393101	0.81[EUR][1000 genomes]
rs35447001	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs35458577	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs35539429	0.81[EUR][1000 genomes]
rs3766077	0.82[EUR][1000 genomes]
rs4589164	0.81[EUR][1000 genomes]
rs4656180	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4656658	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4656661	0.82[EUR][1000 genomes]
rs4656664	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4656665	0.82[EUR][1000 genomes]
rs4656668	0.81[EUR][1000 genomes]
rs4656669	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs61806190	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs61806208	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs61806244	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61808870	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs61808871	0.81[EUR][1000 genomes]
rs61808872	0.82[EUR][1000 genomes]
rs61808874	0.85[EUR][1000 genomes]
rs61808916	0.81[EUR][1000 genomes]
rs61808940	0.81[EUR][1000 genomes]
rs71635617	0.81[EUR][1000 genomes]
rs72700059	0.81[EUR][1000 genomes]
rs745921	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7516097	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7519279	0.85[AMR][1000 genomes];0.86[EUR][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
rs61806242	NME7	cis	Thyroid	GTEx
rs61806242	NME7	Cis_1M	lymphoblastoid	RTeQTL
rs61806242	NME7	cis	Esophagus Muscularis	GTEx
rs61806242	NME7	cis	Artery Tibial	GTEx

Chromatin state (count:13 , 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	chr1:169169600-169175600	Weak transcription	Brain Anterior Caudate	brain
7	chr1:169171600-169184000	Weak transcription	Fetal Intestine Small	intestine
8	chr1:169172000-169176600	Weak transcription	Colon Smooth Muscle	Colon
9	chr1:169172400-169183800	Weak transcription	Brain Germinal Matrix	brain
10	chr1:169172400-169207600	Weak transcription	Esophagus	oesophagus
11	chr1:169172600-169227000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr1:169173200-169202000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr1:169173600-169183800	Weak transcription	Primary hematopoietic stem cells short term culture	blood

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