Variant report

Variant	rs7312164
Chromosome Location	chr12:29475914-29475915
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 65 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs1035604	0.80[ASN][1000 genomes]
rs10843366	0.86[ASN][1000 genomes]
rs10843367	0.86[ASN][1000 genomes]
rs10843371	0.89[ASN][1000 genomes]
rs10843377	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10843382	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10843384	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10843403	0.91[ASN][1000 genomes]
rs11050152	0.81[ASN][1000 genomes]
rs11050157	0.84[ASN][1000 genomes]
rs11050161	0.88[ASN][1000 genomes]
rs11050162	0.88[ASN][1000 genomes]
rs11050167	0.89[ASN][1000 genomes]
rs11050170	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11050173	0.88[ASN][1000 genomes]
rs11050181	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11050187	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11050188	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11050189	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11050190	0.84[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs11050191	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11050192	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11050193	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11050194	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11050208	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12228468	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12231498	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12366505	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12366527	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16934135	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1989478	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1991114	0.80[ASN][1000 genomes]
rs2042511	0.86[ASN][1000 genomes]
rs2194518	0.88[ASN][1000 genomes]
rs2194519	0.89[ASN][1000 genomes]
rs3764953	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3782506	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3782509	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3782511	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4331146	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs57803026	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6487796	0.89[ASN][1000 genomes]
rs6487801	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6487804	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6487805	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6487808	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs67146951	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs67517901	0.89[ASN][1000 genomes]
rs7139273	0.81[EUR][1000 genomes]
rs7294598	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7301188	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7302129	0.89[ASN][1000 genomes]
rs7308125	0.89[ASN][1000 genomes]
rs7311912	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs737160	0.80[EUR][1000 genomes]
rs7954278	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7954871	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7957339	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7973786	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7976961	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs962866	0.81[EUR][1000 genomes]
rs9738721	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7312164	RP11-996F15.2	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:29427200-29527400	Weak transcription	Small Intestine	intestine
2	chr12:29452800-29494200	Weak transcription	Lung	lung
3	chr12:29453800-29480000	Weak transcription	Gastric	stomach
4	chr12:29455200-29489400	Weak transcription	Primary B cells from cord blood	blood
5	chr12:29459400-29493000	Weak transcription	Skeletal Muscle Male	skeletal muscle
6	chr12:29459600-29476000	Weak transcription	Fetal Thymus	thymus
7	chr12:29460200-29476000	Weak transcription	Fetal Stomach	stomach
8	chr12:29461200-29486200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
9	chr12:29462600-29533000	Weak transcription	Aorta	Aorta
10	chr12:29464000-29476000	Weak transcription	Fetal Kidney	kidney
11	chr12:29465000-29494200	Weak transcription	Colonic Mucosa	Colon
12	chr12:29466200-29488800	Weak transcription	Duodenum Smooth Muscle	Duodenum
13	chr12:29468600-29491000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr12:29470000-29486400	Weak transcription	Psoas Muscle	Psoas
15	chr12:29470000-29495600	Weak transcription	Stomach Smooth Muscle	stomach
16	chr12:29470000-29500000	Weak transcription	K562	blood
17	chr12:29470800-29485800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
18	chr12:29470800-29492800	Weak transcription	Primary B cells from peripheral blood	blood
19	chr12:29470800-29492800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr12:29470800-29493400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
21	chr12:29470800-29493800	Weak transcription	Skeletal Muscle Female	skeletal muscle
22	chr12:29470800-29496000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
23	chr12:29470800-29508400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
24	chr12:29470800-29532800	Weak transcription	Right Ventricle	heart
25	chr12:29471200-29477200	Strong transcription	Primary neutrophils fromperipheralblood	blood
26	chr12:29471200-29491400	Weak transcription	Primary T helper cells PMA-I stimulated	--
27	chr12:29471200-29493000	Weak transcription	Brain Substantia Nigra	brain
28	chr12:29471200-29494400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
29	chr12:29471400-29495800	Weak transcription	Brain Anterior Caudate	brain
30	chr12:29471600-29476000	Weak transcription	Fetal Intestine Small	intestine
31	chr12:29471600-29492600	Weak transcription	Duodenum Mucosa	Duodenum
32	chr12:29472200-29493800	Weak transcription	Left Ventricle	heart
33	chr12:29473000-29476000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr12:29473200-29476200	Weak transcription	Fetal Brain Female	brain
35	chr12:29473400-29476000	Strong transcription	Monocytes-CD14+_RO01746	blood
36	chr12:29473800-29485400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr12:29473800-29493000	Weak transcription	HMEC	breast
38	chr12:29473800-29522600	Weak transcription	NHEK	skin
39	chr12:29474000-29476000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr12:29474000-29493400	Weak transcription	HUVEC	blood vessel
41	chr12:29474200-29476200	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr12:29474200-29485200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr12:29474200-29489600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr12:29474200-29490600	Weak transcription	NH-A	brain
45	chr12:29474200-29493000	Weak transcription	Osteobl	bone
46	chr12:29474200-29494200	Weak transcription	NHDF-Ad	bronchial
47	chr12:29474400-29477000	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
48	chr12:29474400-29485600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr12:29474400-29490600	Weak transcription	Liver	Liver
50	chr12:29474600-29476000	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell

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