Variant report

Variant	rs12471312
Chromosome Location	chr2:72789764-72789765
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 185 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:178)

rs_ID	r²[population]
rs10173381	1.00[ASN][1000 genomes]
rs10183056	1.00[CHB][hapmap];0.89[GIH][hapmap]
rs10206555	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap]
rs1032982	0.90[CEU][hapmap];1.00[CHB][hapmap]
rs10460572	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap]
rs10865391	1.00[CHB][hapmap]
rs10865392	1.00[CHD][hapmap];0.89[GIH][hapmap]
rs11126366	1.00[ASN][1000 genomes]
rs11126370	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap]
rs11126373	1.00[CHB][hapmap]
rs11126374	1.00[CHB][hapmap]
rs11126376	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11676555	0.90[CEU][hapmap];1.00[CHB][hapmap]
rs11677707	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[EUR][1000 genomes]
rs11679683	0.90[CEU][hapmap];1.00[CHB][hapmap]
rs11684985	1.00[CHB][hapmap]
rs11685114	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs11686713	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11893504	0.90[EUR][1000 genomes]
rs12052508	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs12471136	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap]
rs12476130	1.00[CHB][hapmap]
rs12476397	1.00[CHB][hapmap]
rs12618390	1.00[CHB][hapmap]
rs12713772	1.00[CHB][hapmap]
rs12713773	1.00[CHB][hapmap]
rs12713774	1.00[CHB][hapmap]
rs12992973	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12996319	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[EUR][1000 genomes]
rs12996406	1.00[CHB][hapmap]
rs12998681	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap]
rs13006497	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs13008041	1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap]
rs13008258	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap]
rs13011477	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13390754	1.00[ASN][1000 genomes]
rs1400581	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1400582	1.00[CHB][hapmap];0.83[GIH][hapmap]
rs1446887	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[EUR][1000 genomes]
rs1446888	1.00[CHB][hapmap];0.88[GIH][hapmap]
rs1446890	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap]
rs1446891	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap]
rs1446892	1.00[CHB][hapmap]
rs1446893	1.00[CHB][hapmap];0.89[GIH][hapmap]
rs1446895	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap]
rs1446896	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[EUR][1000 genomes]
rs1508061	0.90[CEU][hapmap];1.00[CHB][hapmap]
rs1517181	1.00[CHB][hapmap]
rs1517185	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1596930	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1596931	0.95[CEU][hapmap];1.00[CHB][hapmap];0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1711838	1.00[CHB][hapmap]
rs1911690	0.90[CEU][hapmap];1.00[CHB][hapmap]
rs1947118	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2048171	1.00[CHB][hapmap]
rs2138683	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap]
rs2203679	0.90[CEU][hapmap];1.00[CHB][hapmap];0.94[GIH][hapmap];0.98[MKK][hapmap];0.93[TSI][hapmap];1.00[ASN][1000 genomes]
rs2420444	1.00[ASN][1000 genomes]
rs2901146	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs3115351	1.00[CHB][hapmap];0.95[GIH][hapmap];0.84[MKK][hapmap];1.00[ASN][1000 genomes]
rs4364045	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4852291	1.00[CHB][hapmap]
rs4852292	1.00[CHB][hapmap]
rs4852293	1.00[CHB][hapmap]
rs4852294	0.88[EUR][1000 genomes]
rs4852298	1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap]
rs4852872	1.00[CHB][hapmap]
rs4852873	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4852874	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4852875	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap]
rs4852876	1.00[CHB][hapmap]
rs4852877	1.00[CHB][hapmap]
rs4852878	1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap]
rs4852879	1.00[CEU][hapmap];0.95[GIH][hapmap];0.94[MEX][hapmap];0.93[TSI][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4852880	1.00[CHB][hapmap]
rs4852883	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4852886	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap]
rs4852888	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs4852889	0.90[CEU][hapmap];1.00[CHB][hapmap]
rs4852890	0.90[CEU][hapmap];1.00[CHB][hapmap]
rs4852891	0.90[CEU][hapmap];1.00[CHB][hapmap]
rs583119	1.00[ASN][1000 genomes]
rs583673	1.00[CHB][hapmap]
rs584522	1.00[ASN][1000 genomes]
rs585653	1.00[CHB][hapmap]
rs585938	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap]
rs587431	1.00[CHB][hapmap]
rs587744	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs589547	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs590252	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs590345	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs598138	1.00[ASN][1000 genomes]
rs598496	1.00[ASN][1000 genomes]
rs602465	1.00[CHB][hapmap]
rs613880	1.00[CHB][hapmap]
rs614653	1.00[CHB][hapmap]
rs620770	1.00[ASN][1000 genomes]
rs625434	1.00[CHB][hapmap]
rs628432	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs630241	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs632670	1.00[CHB][hapmap];0.89[GIH][hapmap]
rs634476	1.00[CHB][hapmap]
rs634574	1.00[CHB][hapmap]
rs634586	1.00[ASN][1000 genomes]
rs634929	1.00[CHB][hapmap]
rs636734	1.00[CHB][hapmap];0.83[GIH][hapmap]
rs638854	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs640610	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs641123	1.00[CHB][hapmap];0.83[GIH][hapmap]
rs641939	1.00[CHB][hapmap];0.90[GIH][hapmap];1.00[ASN][1000 genomes]
rs642652	1.00[CHB][hapmap];0.95[GIH][hapmap];1.00[LWK][hapmap];0.86[MKK][hapmap];1.00[ASN][1000 genomes]
rs645489	1.00[CHB][hapmap];0.89[GIH][hapmap]
rs646357	1.00[CHB][hapmap]
rs647242	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs647269	1.00[CHB][hapmap]
rs650352	1.00[CHB][hapmap]
rs653220	1.00[ASW][hapmap];0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];1.00[ASN][1000 genomes]
rs6546760	1.00[ASN][1000 genomes]
rs6546764	1.00[ASN][1000 genomes]
rs6546777	1.00[CHB][hapmap]
rs6546778	1.00[CHB][hapmap]
rs6546779	1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap]
rs6546781	0.90[CEU][hapmap];1.00[CHB][hapmap]
rs6546782	1.00[CHB][hapmap]
rs6546783	1.00[CHB][hapmap]
rs656370	1.00[CHB][hapmap]
rs656440	1.00[CHB][hapmap]
rs658067	1.00[CHB][hapmap]
rs659833	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs663218	0.81[ASW][hapmap];1.00[CHB][hapmap];0.95[GIH][hapmap];0.86[MKK][hapmap];1.00[ASN][1000 genomes]
rs666233	1.00[CHB][hapmap];0.90[GIH][hapmap];0.80[MKK][hapmap];1.00[ASN][1000 genomes]
rs666361	1.00[CHB][hapmap]
rs668586	1.00[ASN][1000 genomes]
rs669074	1.00[CHB][hapmap]
rs6714312	1.00[ASN][1000 genomes]
rs6714419	1.00[ASN][1000 genomes]
rs6714595	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs671721	1.00[CHB][hapmap];0.89[GIH][hapmap]
rs6724529	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs6737565	1.00[ASN][1000 genomes]
rs6742312	1.00[CHB][hapmap]
rs6747378	1.00[CHB][hapmap]
rs674863	1.00[CHB][hapmap]
rs6750766	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap]
rs6752122	1.00[ASN][1000 genomes]
rs6758593	1.00[ASW][hapmap];0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];1.00[ASN][1000 genomes]
rs678684	1.00[CHB][hapmap]
rs680380	1.00[CHB][hapmap]
rs680495	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs681574	1.00[CHB][hapmap]
rs683328	1.00[CHB][hapmap]
rs684673	1.00[CHB][hapmap]
rs687325	1.00[CHB][hapmap]
rs688433	1.00[CHB][hapmap];0.89[GIH][hapmap]
rs689154	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs7420588	1.00[ASN][1000 genomes]
rs7420667	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7558686	1.00[ASN][1000 genomes]
rs7558919	1.00[ASN][1000 genomes]
rs7560529	1.00[CHB][hapmap]
rs7563738	1.00[ASN][1000 genomes]
rs7565198	1.00[CHB][hapmap]
rs7568803	1.00[ASN][1000 genomes]
rs7571064	1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap]
rs7577238	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7580268	1.00[CHB][hapmap]
rs7588400	0.90[CEU][hapmap];1.00[CHB][hapmap]
rs7591025	1.00[CHB][hapmap]
rs7591303	1.00[CHB][hapmap];0.83[GIH][hapmap]
rs7594350	1.00[ASN][1000 genomes]
rs7595180	1.00[ASN][1000 genomes]
rs7595315	1.00[ASN][1000 genomes]
rs7598238	1.00[CHB][hapmap]
rs7600273	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7601020	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap]
rs7601318	1.00[CHB][hapmap]
rs983928	1.00[CHB][hapmap]
rs990569	1.00[CHB][hapmap];1.00[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv963919	chr2:72372956-72830387	Enhancers Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv1005487	chr2:72464784-72819704	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv1008335	chr2:72561463-72819704	ZNF genes & repeats Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv874264	chr2:72593243-72901170	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv582208	chr2:72690622-72835886	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	nsv834257	chr2:72701083-72853548	Enhancers Weak transcription ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	nsv874265	chr2:72789764-72982609	Enhancers ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12471312	MPHOSPH10	cis	cerebellum	SCAN
rs12471312	TGFA	cis	cerebellum	SCAN
rs12471312	AUP1	cis	parietal	SCAN
rs12471312	STAMBP	cis	cerebellum	SCAN

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:72775000-72808800	Weak transcription	Ovary	ovary
2	chr2:72783400-72792200	Weak transcription	Left Ventricle	heart
3	chr2:72783600-72793600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
4	chr2:72784000-72800800	Weak transcription	Placenta	Placenta
5	chr2:72784200-72799600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr2:72786000-72803800	Weak transcription	Primary T helper cells PMA-I stimulated	--
7	chr2:72787600-72791000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr2:72788000-72789800	Enhancers	Rectal Smooth Muscle	rectum
9	chr2:72788000-72790600	Enhancers	Hela-S3	cervix
10	chr2:72788200-72790000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr2:72788600-72789800	Enhancers	HUES48 Cell Line	embryonic stem cell
12	chr2:72788600-72789800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr2:72788600-72789800	Enhancers	NHDF-Ad	bronchial
14	chr2:72788600-72790000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr2:72788600-72790000	Enhancers	HUES64 Cell Line	embryonic stem cell
16	chr2:72788600-72790000	Enhancers	iPS-20b Cell Line	embryonic stem cell
17	chr2:72788600-72790000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr2:72788600-72790000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr2:72788600-72790000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr2:72788600-72790000	Enhancers	Fetal Heart	heart
21	chr2:72788600-72790000	Enhancers	HSMM	muscle
22	chr2:72788600-72790200	Enhancers	Aorta	Aorta
23	chr2:72788600-72790200	Enhancers	Brain Hippocampus Middle	brain
24	chr2:72788600-72790200	Enhancers	NHLF	lung
25	chr2:72788600-72790600	Enhancers	NH-A	brain
26	chr2:72788800-72789800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr2:72788800-72789800	Enhancers	Brain Cingulate Gyrus	brain
28	chr2:72788800-72789800	Flanking Active TSS	HUVEC	blood vessel
29	chr2:72788800-72790000	Enhancers	ES-I3 Cell Line	embryonic stem cell
30	chr2:72788800-72790000	Enhancers	iPS-15b Cell Line	embryonic stem cell
31	chr2:72788800-72790000	Enhancers	Placenta Amnion	Placenta Amnion
32	chr2:72788800-72790000	Flanking Active TSS	A549	lung
33	chr2:72788800-72790000	Enhancers	HMEC	breast
34	chr2:72788800-72790400	Enhancers	Colon Smooth Muscle	Colon
35	chr2:72788800-72790400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
36	chr2:72789000-72789800	Enhancers	H1 Cell Line	embryonic stem cell
37	chr2:72789000-72789800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr2:72789000-72789800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr2:72789000-72789800	Enhancers	Brain Angular Gyrus	brain
40	chr2:72789000-72789800	Enhancers	Skeletal Muscle Female	skeletal muscle
41	chr2:72789000-72790000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr2:72789000-72792200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
43	chr2:72789200-72789800	Enhancers	K562	blood
44	chr2:72789200-72789800	Enhancers	NHEK	skin
45	chr2:72789200-72790000	Enhancers	HUES6 Cell Line	embryonic stem cell
46	chr2:72789200-72790000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr2:72789200-72790200	Enhancers	Brain Substantia Nigra	brain
48	chr2:72789200-72790600	Enhancers	Primary hematopoietic stem cells	blood
49	chr2:72789200-72790600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
50	chr2:72789200-72803600	Weak transcription	Duodenum Smooth Muscle	Duodenum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links