Variant report

Variant	rs12408636
Chromosome Location	chr1:169184598-169184599
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:169177420..169179762-chr1:169182344..169184753,2	MCF-7	breast:

Extended variants
information (count: 78 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs1018832	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10458388	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10458394	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10489190	1.00[AFR][1000 genomes]
rs10489417	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10494477	1.00[AFR][1000 genomes]
rs10494478	1.00[AFR][1000 genomes]
rs10800433	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10919070	0.82[AMR][1000 genomes]
rs10919071	0.82[AMR][1000 genomes]
rs10919074	0.86[AMR][1000 genomes]
rs10919085	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10919087	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10919093	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10919114	0.86[ASN][1000 genomes]
rs10919122	1.00[AFR][1000 genomes]
rs10919123	1.00[AFR][1000 genomes]
rs10919125	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10919127	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10919128	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10919147	1.00[AFR][1000 genomes]
rs10919149	1.00[AFR][1000 genomes]
rs10919150	1.00[AFR][1000 genomes]
rs10919153	1.00[AFR][1000 genomes]
rs10919158	1.00[AFR][1000 genomes]
rs10919162	1.00[AFR][1000 genomes]
rs10919165	1.00[AFR][1000 genomes]
rs12021696	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12022617	1.00[AFR][1000 genomes]
rs12025566	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12025721	1.00[AFR][1000 genomes]
rs12028197	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12029800	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12029857	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12030541	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12030810	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12031371	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12035622	0.86[AMR][1000 genomes]
rs12036426	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12037926	1.00[AFR][1000 genomes]
rs12042082	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12042990	1.00[AFR][1000 genomes]
rs12044982	1.00[AFR][1000 genomes]
rs12045803	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12048188	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12401962	1.00[AFR][1000 genomes]
rs12401966	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12403181	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12405185	1.00[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs12405725	1.00[AFR][1000 genomes]
rs12406341	0.86[AMR][1000 genomes]
rs12410241	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12410387	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12410456	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12410548	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12567342	1.00[AFR][1000 genomes]
rs17345156	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs17345426	1.00[AFR][1000 genomes]
rs17345531	1.00[AFR][1000 genomes]
rs17349677	1.00[AFR][1000 genomes]
rs2000321	0.83[AMR][1000 genomes]
rs2001155	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2001156	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34323371	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3766074	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3766101	1.00[AFR][1000 genomes]
rs4497270	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4562680	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs72706963	0.83[AMR][1000 genomes]
rs72706975	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7528142	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7556463	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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	nsv429913	chr1:169177019-169296744	Weak transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Strong transcription Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	esv1834321	chr1:169180302-169240975	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	esv1845262	chr1:169180302-169240975	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12408636	NME7	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:169130400-169195200	Weak transcription	Pancreas	Pancrea
2	chr1:169167800-169186800	Weak transcription	Primary T cells from cord blood	blood
3	chr1:169172400-169207600	Weak transcription	Esophagus	oesophagus
4	chr1:169172600-169227000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr1:169173200-169202000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr1:169176600-169206200	Weak transcription	Aorta	Aorta
7	chr1:169177400-169207400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr1:169178600-169191400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr1:169180000-169210000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr1:169180600-169206200	Weak transcription	Left Ventricle	heart
11	chr1:169181400-169185400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr1:169182000-169184600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
13	chr1:169182000-169185400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr1:169182000-169201000	Weak transcription	Cortex derived primary cultured neurospheres	brain
15	chr1:169182800-169192000	Weak transcription	Small Intestine	intestine
16	chr1:169182800-169205400	Weak transcription	Adipose Nuclei	Adipose
17	chr1:169183600-169187200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr1:169183800-169184600	Strong transcription	Primary B cells from cord blood	blood
19	chr1:169183800-169184600	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
20	chr1:169183800-169184600	ZNF genes & repeats	Brain Germinal Matrix	brain
21	chr1:169183800-169184800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr1:169183800-169184800	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr1:169184000-169184600	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
24	chr1:169184000-169184800	ZNF genes & repeats	Primary hematopoietic stem cells	blood
25	chr1:169184000-169184800	ZNF genes & repeats	Ovary	ovary
26	chr1:169184000-169198800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr1:169184200-169184600	Strong transcription	Fetal Stomach	stomach
28	chr1:169184200-169185000	ZNF genes & repeats	Fetal Intestine Small	intestine
29	chr1:169184200-169185600	Weak transcription	Gastric	stomach
30	chr1:169184400-169206200	Weak transcription	Lung	lung

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