Variant report

Variant	rs4852883
Chromosome Location	chr2:72855023-72855024
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 159 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:157)

rs_ID	r²[population]
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];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
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]
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];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11676555	0.90[CEU][hapmap];1.00[CHB][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11677707	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11679683	0.90[CEU][hapmap];1.00[CHB][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11684985	1.00[CHB][hapmap]
rs11685114	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
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];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11893504	0.83[EUR][1000 genomes]
rs11898717	0.82[YRI][hapmap]
rs12052508	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs12468173	0.87[EUR][1000 genomes]
rs12468179	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12471136	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap]
rs12471312	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]
rs12476130	1.00[CHB][hapmap]
rs12476397	1.00[CHB][hapmap]
rs12617074	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12618390	1.00[CHB][hapmap]
rs12713772	1.00[CHB][hapmap]
rs12713773	1.00[CHB][hapmap]
rs12713774	1.00[CHB][hapmap]
rs12713775	1.00[CHD][hapmap]
rs12992973	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12996319	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12996406	1.00[CHB][hapmap]
rs12998681	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap]
rs13006497	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
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];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1400581	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs1446887	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[AMR][1000 genomes];0.95[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];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1508061	0.90[CEU][hapmap];1.00[CHB][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1517181	1.00[CHB][hapmap]
rs1517185	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs1596930	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1596931	0.95[CEU][hapmap];1.00[CHB][hapmap];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1711838	1.00[CHB][hapmap]
rs17503444	1.00[CHB][hapmap]
rs1911690	0.90[CEU][hapmap];1.00[CHB][hapmap];0.81[EUR][1000 genomes]
rs1947118	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1995734	1.00[CHB][hapmap]
rs2048171	1.00[CHB][hapmap]
rs2063170	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
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];0.93[TSI][hapmap];1.00[ASN][1000 genomes]
rs2901146	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs3115351	1.00[ASN][1000 genomes]
rs4364045	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4852291	1.00[CHB][hapmap]
rs4852292	1.00[CHB][hapmap]
rs4852293	1.00[CHB][hapmap]
rs4852294	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4852298	1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap]
rs4852872	1.00[CHB][hapmap]
rs4852873	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4852874	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[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	0.92[ASW][hapmap];1.00[CEU][hapmap];0.95[GIH][hapmap];0.94[MEX][hapmap];0.86[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.90[EUR][1000 genomes]
rs4852880	1.00[CHB][hapmap]
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];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4852888	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4852889	0.90[CEU][hapmap];1.00[CHB][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4852890	0.90[CEU][hapmap];1.00[CHB][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4852891	0.90[CEU][hapmap];1.00[CHB][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
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]
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[ASN][1000 genomes]
rs590345	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs620770	1.00[ASN][1000 genomes]
rs628432	1.00[ASN][1000 genomes]
rs630241	1.00[ASN][1000 genomes]
rs632670	1.00[CHB][hapmap];0.89[GIH][hapmap]
rs634586	1.00[ASN][1000 genomes]
rs634929	1.00[CHB][hapmap]
rs638854	1.00[ASN][1000 genomes]
rs640610	1.00[ASN][1000 genomes]
rs641939	1.00[ASN][1000 genomes]
rs642652	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	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]
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];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
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[ASN][1000 genomes]
rs663218	1.00[CHB][hapmap];0.95[GIH][hapmap];1.00[ASN][1000 genomes]
rs666361	1.00[CHB][hapmap]
rs668586	1.00[ASN][1000 genomes]
rs6708156	0.88[AMR][1000 genomes];0.88[EUR][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];0.83[AMR][1000 genomes];0.84[EUR][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]
rs6758593	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];1.00[ASN][1000 genomes]
rs678684	1.00[CHB][hapmap]
rs680380	1.00[CHB][hapmap]
rs683328	1.00[CHB][hapmap]
rs684673	1.00[CHB][hapmap]
rs688433	1.00[CHB][hapmap];0.89[GIH][hapmap]
rs689154	1.00[ASN][1000 genomes]
rs7420588	1.00[ASN][1000 genomes]
rs7420667	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7560529	1.00[CHB][hapmap]
rs7563738	1.00[ASN][1000 genomes]
rs7565198	1.00[CHB][hapmap]
rs7571064	1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap]
rs7577238	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[EUR][1000 genomes]
rs7580268	1.00[CHB][hapmap]
rs7588400	0.90[CEU][hapmap];1.00[CHB][hapmap];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7588602	1.00[CHB][hapmap]
rs7591025	1.00[CHB][hapmap]
rs7591303	1.00[CHB][hapmap];0.83[GIH][hapmap]
rs7592155	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs7598238	1.00[CHB][hapmap]
rs7600273	0.94[AMR][1000 genomes];1.00[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:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
rs4852883	TGFA	cis	cerebellum	SCAN
rs4852883	MPHOSPH10	cis	cerebellum	SCAN
rs4852883	STAMBP	cis	cerebellum	SCAN
rs4852883	AUP1	cis	parietal	SCAN

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:72840200-72878600	Weak transcription	Aorta	Aorta
2	chr2:72843800-72866200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr2:72845000-72862400	Weak transcription	Fetal Intestine Small	intestine
4	chr2:72847200-72856200	Weak transcription	Brain Substantia Nigra	brain
5	chr2:72847400-72855200	Weak transcription	Left Ventricle	heart
6	chr2:72847400-72857200	Weak transcription	Right Ventricle	heart
7	chr2:72847400-72865600	Weak transcription	Right Atrium	heart
8	chr2:72847400-72865800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr2:72847400-72869000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr2:72851000-72857200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr2:72853000-72855800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr2:72853200-72855600	Weak transcription	Brain Anterior Caudate	brain
13	chr2:72853200-72857400	Weak transcription	Brain Angular Gyrus	brain
14	chr2:72853800-72856000	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr2:72854200-72868400	Weak transcription	Fetal Stomach	stomach
16	chr2:72854400-72857200	Weak transcription	Brain Hippocampus Middle	brain
17	chr2:72854600-72855800	Weak transcription	Skeletal Muscle Female	skeletal muscle
18	chr2:72855000-72855600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr2:72855000-72855600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
20	chr2:72855000-72855800	Weak transcription	Ovary	ovary
21	chr2:72855000-72856000	Weak transcription	Adipose Nuclei	Adipose
22	chr2:72855000-72857800	Weak transcription	Fetal Lung	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links