Variant report

Variant	rs1006409
Chromosome Location	chr12:29435675-29435676
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 13 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs10771508	0.81[YRI][hapmap]
rs10771511	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10843375	0.84[AFR][1000 genomes]
rs2015599	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2216853	0.81[YRI][hapmap]
rs2216854	0.80[LWK][hapmap]
rs7139273	0.83[CHB][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes]
rs7316004	0.82[YRI][hapmap]
rs737160	0.93[ASW][hapmap];0.83[CHB][hapmap];0.92[LWK][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes]
rs962866	0.83[CHB][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532233	chr12:29009388-29496179	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv995123	chr12:29095272-29571558	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
3	nsv1053641	chr12:29268813-29854413	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:29417200-29465400	Weak transcription	Rectal Mucosa Donor 29	rectum
2	chr12:29422000-29455600	Weak transcription	Left Ventricle	heart
3	chr12:29422000-29465000	Weak transcription	Duodenum Smooth Muscle	Duodenum
4	chr12:29426600-29440600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr12:29426800-29436200	Weak transcription	Duodenum Mucosa	Duodenum
6	chr12:29426800-29440600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr12:29426800-29472800	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr12:29427000-29452200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr12:29427200-29527400	Weak transcription	Small Intestine	intestine
10	chr12:29427800-29438400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
11	chr12:29429000-29460200	Weak transcription	Primary T cells from cord blood	blood
12	chr12:29429200-29463600	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr12:29429400-29460400	Weak transcription	Monocytes-CD14+_RO01746	blood
14	chr12:29432200-29442800	Weak transcription	Psoas Muscle	Psoas
15	chr12:29432400-29438400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr12:29432600-29436600	Weak transcription	NH-A	brain
17	chr12:29432800-29445800	Weak transcription	Primary B cells from cord blood	blood
18	chr12:29433400-29436000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr12:29433400-29436400	Enhancers	Primary hematopoietic stem cells	blood
20	chr12:29434200-29449600	Weak transcription	Primary neutrophils fromperipheralblood	blood
21	chr12:29434400-29435800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr12:29434400-29435800	Enhancers	Adipose Nuclei	Adipose
23	chr12:29434400-29439000	Enhancers	Osteobl	bone
24	chr12:29434600-29436200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr12:29434800-29436000	Enhancers	Dnd41	blood
26	chr12:29434800-29436000	Enhancers	HSMM	muscle
27	chr12:29435000-29436000	Enhancers	HUVEC	blood vessel
28	chr12:29435200-29436000	Enhancers	NHDF-Ad	bronchial
29	chr12:29435400-29436800	Enhancers	Primary hematopoietic stem cells short term culture	blood
30	chr12:29435400-29436800	Weak transcription	Muscle Satellite Cultured Cells	--
31	chr12:29435400-29439000	Weak transcription	HSMMtube	muscle
32	chr12:29435400-29439600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr12:29435400-29467200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
34	chr12:29435600-29435800	Enhancers	Brain Hippocampus Middle	brain
35	chr12:29435600-29436600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links