Variant report

Variant	rs7979654
Chromosome Location	chr12:29432138-29432139
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 74 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs10492383	0.93[CEU][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11608616	0.91[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11609540	0.92[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11610197	0.84[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11610910	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11611420	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11611687	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11612172	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11613628	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11614129	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11614901	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11615636	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12314737	0.80[CEU][hapmap]
rs12809077	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12809493	0.80[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs12810064	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12810315	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12811201	0.84[ASN][1000 genomes]
rs12811723	0.92[CEU][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12813520	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12813731	0.90[ASN][1000 genomes]
rs12813789	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12813996	1.00[CEU][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12814180	0.92[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12814930	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12815222	0.93[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12816511	1.00[CEU][hapmap];0.90[YRI][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12817163	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12817578	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12817825	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12817985	0.81[YRI][hapmap];0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12819896	0.92[CEU][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12821498	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12821559	0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12821708	1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12822770	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12823372	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12823422	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12823485	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12823903	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12824407	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12826064	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12829666	0.91[CEU][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12830274	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12830493	0.93[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12830678	0.93[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12830906	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12831730	0.92[CEU][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12832038	0.93[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12832263	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16934061	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1988943	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2350312	0.90[YRI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2882377	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs34162895	0.95[AMR][1000 genomes]
rs35618989	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35636563	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs36126531	1.00[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3764952	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4369447	1.00[CEU][hapmap];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs67280216	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs67324531	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7134744	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7295387	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7299158	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7299635	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7299663	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7308372	0.93[CEU][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7314594	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7961336	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7964254	0.98[AMR][1000 genomes];0.97[EUR][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

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs7979654	RP11-996F15.2	cis	Esophagus Mucosa	GTEx
rs7979654	RP11-996F15.2	cis	Nerve Tibial	GTEx
rs7979654	RP11-996F15.2	cis	Skin Sun Exposed Lower leg	GTEx
rs7979654	RP11-996F15.2	cis	Artery Tibial	GTEx
rs7979654	RP11-996F15.2	cis	Thyroid	GTEx
rs7979654	RP11-996F15.2	cis	lung	GTEx
rs7979654	RP11-996F15.2	cis	Adipose Subcutaneous	GTEx
rs7979654	RP11-996F15.2	cis	Esophagus Muscularis	GTEx

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:29414400-29434000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr12:29417200-29465400	Weak transcription	Rectal Mucosa Donor 29	rectum
3	chr12:29420400-29435000	Weak transcription	HUVEC	blood vessel
4	chr12:29422000-29455600	Weak transcription	Left Ventricle	heart
5	chr12:29422000-29465000	Weak transcription	Duodenum Smooth Muscle	Duodenum
6	chr12:29422200-29434800	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr12:29422400-29434400	Weak transcription	Fetal Kidney	kidney
8	chr12:29424600-29435200	Weak transcription	Colon Smooth Muscle	Colon
9	chr12:29424800-29433400	Weak transcription	Primary hematopoietic stem cells	blood
10	chr12:29424800-29434800	Weak transcription	Dnd41	blood
11	chr12:29425000-29434400	Weak transcription	Fetal Stomach	stomach
12	chr12:29425200-29435600	Weak transcription	Brain Hippocampus Middle	brain
13	chr12:29426600-29434400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr12:29426600-29440600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr12:29426800-29432200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr12:29426800-29433600	Weak transcription	Fetal Muscle Trunk	muscle
17	chr12:29426800-29436200	Weak transcription	Duodenum Mucosa	Duodenum
18	chr12:29426800-29440600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr12:29426800-29472800	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr12:29427000-29433600	Weak transcription	Spleen	Spleen
21	chr12:29427000-29435200	Weak transcription	Primary monocytes fromperipheralblood	blood
22	chr12:29427000-29452200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr12:29427200-29527400	Weak transcription	Small Intestine	intestine
24	chr12:29427800-29438400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
25	chr12:29428600-29434200	Strong transcription	Primary neutrophils fromperipheralblood	blood
26	chr12:29429000-29433400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
27	chr12:29429000-29460200	Weak transcription	Primary T cells from cord blood	blood
28	chr12:29429200-29463600	Weak transcription	Rectal Mucosa Donor 31	rectum
29	chr12:29429400-29460400	Weak transcription	Monocytes-CD14+_RO01746	blood
30	chr12:29430200-29432600	Enhancers	NH-A	brain
31	chr12:29430200-29432800	Enhancers	NHDF-Ad	bronchial
32	chr12:29431200-29432800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr12:29431200-29433400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr12:29431400-29432200	Enhancers	Fetal Muscle Leg	muscle
35	chr12:29431400-29432600	Enhancers	Muscle Satellite Cultured Cells	--
36	chr12:29431400-29432600	Enhancers	HSMM	muscle
37	chr12:29431400-29432800	Enhancers	Osteobl	bone
38	chr12:29431400-29433400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr12:29431600-29432400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
40	chr12:29431600-29432600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr12:29431800-29432200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr12:29431800-29432800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr12:29431800-29434800	Weak transcription	HSMMtube	muscle
44	chr12:29432000-29432400	Enhancers	Adipose Nuclei	Adipose
45	chr12:29432000-29432400	Enhancers	Rectal Smooth Muscle	rectum
46	chr12:29432000-29432400	Enhancers	NHLF	lung
47	chr12:29432000-29432800	Genic enhancers	Primary hematopoietic stem cells short term culture	blood

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