Variant report

Variant	rs7299283
Chromosome Location	chr12:29430375-29430376
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 45 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs1006410	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1072724	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10743652	0.82[CHB][hapmap];0.87[YRI][hapmap]
rs10743656	0.81[CEU][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10771514	0.95[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10771517	0.83[EUR][1000 genomes]
rs10843376	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10843385	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10843399	0.93[JPT][hapmap];0.81[ASN][1000 genomes]
rs11050147	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11050149	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11050168	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12301475	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12578931	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12581107	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17715086	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1836861	0.93[JPT][hapmap]
rs2016832	0.95[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2288128	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2288129	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2350315	0.80[CHB][hapmap];0.85[JPT][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3782505	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3782510	1.00[CEU][hapmap];0.85[CHB][hapmap];0.93[JPT][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3948497	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4277150	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4931171	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4931174	0.82[ASN][1000 genomes]
rs6487807	0.84[CEU][hapmap];0.95[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7137141	0.82[AFR][1000 genomes]
rs7298031	0.81[CEU][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs73063614	0.82[AFR][1000 genomes]
rs7308534	0.92[YRI][hapmap]
rs7313552	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7315346	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7358667	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7953619	1.00[YRI][hapmap]
rs7956305	0.81[CEU][hapmap];0.95[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7959145	0.95[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7961943	0.95[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7964831	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7980218	0.93[YRI][hapmap];0.95[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs986072	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7299283	RP11-996F15.2	cis	Nerve Tibial	GTEx
rs7299283	RP11-996F15.2	cis	Thyroid	GTEx
rs7299283	RP11-996F15.2	cis	lung	GTEx

Chromatin state (count:46 , 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	chr12:29419200-29430600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr12:29419800-29430400	Weak transcription	Brain Angular Gyrus	brain
5	chr12:29420400-29435000	Weak transcription	HUVEC	blood vessel
6	chr12:29420600-29431600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr12:29421000-29432000	Weak transcription	Adipose Nuclei	Adipose
8	chr12:29422000-29455600	Weak transcription	Left Ventricle	heart
9	chr12:29422000-29465000	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr12:29422200-29430400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr12:29422200-29434800	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr12:29422400-29434400	Weak transcription	Fetal Kidney	kidney
13	chr12:29424600-29435200	Weak transcription	Colon Smooth Muscle	Colon
14	chr12:29424800-29433400	Weak transcription	Primary hematopoietic stem cells	blood
15	chr12:29424800-29434800	Weak transcription	Dnd41	blood
16	chr12:29425000-29434400	Weak transcription	Fetal Stomach	stomach
17	chr12:29425200-29435600	Weak transcription	Brain Hippocampus Middle	brain
18	chr12:29426200-29430600	Weak transcription	Fetal Intestine Large	intestine
19	chr12:29426200-29430800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr12:29426600-29431400	Weak transcription	Fetal Muscle Leg	muscle
21	chr12:29426600-29434400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr12:29426600-29440600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr12:29426800-29430400	Weak transcription	Fetal Intestine Small	intestine
24	chr12:29426800-29432200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr12:29426800-29433600	Weak transcription	Fetal Muscle Trunk	muscle
26	chr12:29426800-29436200	Weak transcription	Duodenum Mucosa	Duodenum
27	chr12:29426800-29440600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr12:29426800-29472800	Weak transcription	Sigmoid Colon	Sigmoid Colon
29	chr12:29427000-29431200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr12:29427000-29433600	Weak transcription	Spleen	Spleen
31	chr12:29427000-29435200	Weak transcription	Primary monocytes fromperipheralblood	blood
32	chr12:29427000-29452200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr12:29427200-29527400	Weak transcription	Small Intestine	intestine
34	chr12:29427800-29432000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr12:29427800-29438400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
36	chr12:29428600-29434200	Strong transcription	Primary neutrophils fromperipheralblood	blood
37	chr12:29429000-29432000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
38	chr12:29429000-29433400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
39	chr12:29429000-29460200	Weak transcription	Primary T cells from cord blood	blood
40	chr12:29429200-29463600	Weak transcription	Rectal Mucosa Donor 31	rectum
41	chr12:29429400-29460400	Weak transcription	Monocytes-CD14+_RO01746	blood
42	chr12:29430200-29430400	Enhancers	Osteobl	bone
43	chr12:29430200-29430600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr12:29430200-29430600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr12:29430200-29432600	Enhancers	NH-A	brain
46	chr12:29430200-29432800	Enhancers	NHDF-Ad	bronchial

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