Variant report

Variant	rs4852286
Chromosome Location	chr2:72502993-72502994
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 156 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:154)

rs_ID	r²[population]
rs1000523	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10168145	1.00[CHB][hapmap]
rs10173381	1.00[CHB][hapmap]
rs10175915	0.91[GIH][hapmap];1.00[MEX][hapmap];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10178138	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10178847	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10181899	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10186080	1.00[CHB][hapmap]
rs10190674	1.00[CHB][hapmap]
rs10192800	1.00[CHB][hapmap]
rs10193543	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10203965	1.00[CHB][hapmap]
rs10204415	1.00[CHB][hapmap];0.95[GIH][hapmap];0.87[MEX][hapmap];0.85[TSI][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10205108	0.87[GIH][hapmap]
rs10207299	1.00[CHB][hapmap]
rs10221767	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10221769	0.87[GIH][hapmap]
rs11126366	1.00[CHB][hapmap]
rs1123199	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1159764	0.87[GIH][hapmap]
rs1159766	0.87[GIH][hapmap]
rs11690734	1.00[CHB][hapmap]
rs11694921	1.00[CHB][hapmap]
rs11902025	1.00[CHB][hapmap]
rs12463825	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12466026	0.81[EUR][1000 genomes]
rs12466112	0.81[EUR][1000 genomes]
rs12466613	1.00[CHB][hapmap]
rs12467816	1.00[CHB][hapmap]
rs12468057	1.00[CHB][hapmap]
rs12471875	1.00[CHB][hapmap]
rs12476397	1.00[CHB][hapmap]
rs13382986	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13383535	1.00[CHB][hapmap]
rs13387630	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13389524	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13390754	1.00[CHB][hapmap]
rs13392314	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13409513	1.00[CHB][hapmap]
rs13409641	1.00[CHB][hapmap];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13417114	0.83[GIH][hapmap];0.82[MEX][hapmap]
rs13430254	0.82[EUR][1000 genomes]
rs13430651	0.82[EUR][1000 genomes]
rs13432350	1.00[CHB][hapmap];0.91[GIH][hapmap]
rs1400582	1.00[CHB][hapmap]
rs1568145	1.00[CHB][hapmap]
rs17673916	0.87[GIH][hapmap];1.00[MEX][hapmap];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs17724205	0.81[EUR][1000 genomes]
rs17724860	0.91[GIH][hapmap];1.00[MEX][hapmap];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs17725024	0.91[GIH][hapmap];1.00[MEX][hapmap];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2080044	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2109960	1.00[CHB][hapmap]
rs2159823	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2192014	1.00[CHB][hapmap]
rs2192015	1.00[CHB][hapmap]
rs2203679	1.00[CHB][hapmap]
rs2420444	1.00[CHB][hapmap]
rs2901146	1.00[CHB][hapmap]
rs3115351	1.00[CHB][hapmap]
rs41386	0.91[GIH][hapmap];0.87[MEX][hapmap]
rs41388	0.87[GIH][hapmap]
rs41389	0.87[GIH][hapmap]
rs41393	0.87[GIH][hapmap]
rs41394	0.87[GIH][hapmap]
rs41398	0.83[GIH][hapmap]
rs41403	0.87[GIH][hapmap]
rs41407	0.87[GIH][hapmap]
rs41412	0.83[GIH][hapmap]
rs41415	0.87[GIH][hapmap];0.93[MEX][hapmap]
rs41416	0.87[GIH][hapmap];0.93[MEX][hapmap]
rs41417	0.91[GIH][hapmap];0.93[MEX][hapmap]
rs4852287	1.00[CHB][hapmap]
rs4852288	1.00[CHB][hapmap];0.91[GIH][hapmap]
rs4852859	0.82[EUR][1000 genomes]
rs55764675	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs55970539	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs56045434	0.87[AMR][1000 genomes]
rs56143801	0.89[AMR][1000 genomes]
rs56299443	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs585653	1.00[CHB][hapmap]
rs587431	1.00[CHB][hapmap]
rs587744	1.00[CHB][hapmap]
rs589547	1.00[CHB][hapmap]
rs590252	1.00[CHB][hapmap]
rs590345	1.00[CHB][hapmap]
rs598138	1.00[CHB][hapmap]
rs598496	1.00[CHB][hapmap]
rs602465	1.00[CHB][hapmap]
rs613880	1.00[CHB][hapmap]
rs614653	1.00[CHB][hapmap]
rs62147573	0.81[EUR][1000 genomes]
rs62147589	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs62147626	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs62147629	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs62147636	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs62149273	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs625434	1.00[CHB][hapmap]
rs628432	1.00[CHB][hapmap]
rs630241	1.00[CHB][hapmap]
rs634476	1.00[CHB][hapmap]
rs634574	1.00[CHB][hapmap]
rs634785	1.00[CHB][hapmap]
rs634929	1.00[CHB][hapmap]
rs636319	1.00[CHB][hapmap]
rs636734	1.00[CHB][hapmap]
rs638854	1.00[CHB][hapmap]
rs640610	1.00[CHB][hapmap]
rs641123	1.00[CHB][hapmap]
rs641939	1.00[CHB][hapmap]
rs642652	1.00[CHB][hapmap]
rs645489	1.00[CHB][hapmap]
rs646357	1.00[CHB][hapmap]
rs647242	1.00[CHB][hapmap]
rs647269	1.00[CHB][hapmap]
rs6546756	1.00[CHB][hapmap]
rs6546760	1.00[CHB][hapmap]
rs6546764	1.00[CHB][hapmap]
rs6546765	1.00[CHB][hapmap]
rs656370	1.00[CHB][hapmap]
rs656440	1.00[CHB][hapmap]
rs658067	1.00[CHB][hapmap]
rs659833	1.00[CHB][hapmap]
rs663218	1.00[CHB][hapmap]
rs666233	1.00[CHB][hapmap]
rs666361	1.00[CHB][hapmap]
rs669074	1.00[CHB][hapmap]
rs6711257	0.81[EUR][1000 genomes]
rs6719255	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6729863	1.00[CHB][hapmap]
rs6733210	1.00[CHB][hapmap]
rs6742264	1.00[CHB][hapmap]
rs674863	1.00[CHB][hapmap]
rs6752122	1.00[CHB][hapmap]
rs6753073	1.00[CHB][hapmap]
rs6758462	1.00[CHB][hapmap]
rs678684	1.00[CHB][hapmap]
rs680380	1.00[CHB][hapmap]
rs680495	1.00[CHB][hapmap]
rs681574	1.00[CHB][hapmap]
rs687325	1.00[CHB][hapmap]
rs687371	1.00[CHB][hapmap]
rs688433	1.00[CHB][hapmap]
rs689154	1.00[CHB][hapmap]
rs719117	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7558686	1.00[CHB][hapmap]
rs7558919	1.00[CHB][hapmap]
rs7559131	1.00[CHB][hapmap];0.91[GIH][hapmap]
rs7568803	1.00[CHB][hapmap]
rs7577877	1.00[CHB][hapmap]
rs7583271	1.00[CHB][hapmap];0.91[GIH][hapmap]
rs7594350	1.00[CHB][hapmap]
rs7595180	1.00[CHB][hapmap]
rs7603966	1.00[CHB][hapmap]
rs9309464	1.00[CHB][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	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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4852286	BOLA3	cis	parietal	SCAN
rs4852286	CCT7	cis	parietal	SCAN
rs4852286	CYP26B1	cis	Whole Blood	GTEx
rs4852286	FBXO48	cis	cerebellum	SCAN

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:72489200-72508200	Weak transcription	Aorta	Aorta
2	chr2:72497200-72503400	Enhancers	Fetal Intestine Large	intestine
3	chr2:72497400-72505400	Weak transcription	Skeletal Muscle Male	skeletal muscle
4	chr2:72498000-72503000	Enhancers	Fetal Intestine Small	intestine
5	chr2:72499400-72503000	Weak transcription	Left Ventricle	heart
6	chr2:72499400-72507800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr2:72499400-72507800	Weak transcription	Psoas Muscle	Psoas
8	chr2:72499600-72510400	Weak transcription	Right Ventricle	heart
9	chr2:72499800-72505200	Weak transcription	NHEK	skin
10	chr2:72500600-72503600	Enhancers	Brain Substantia Nigra	brain
11	chr2:72501000-72503000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr2:72501000-72505800	Weak transcription	Pancreas	Pancrea
13	chr2:72501600-72503400	Enhancers	Fetal Heart	heart
14	chr2:72501600-72503400	Weak transcription	NH-A	brain
15	chr2:72501600-72503600	Enhancers	Brain Hippocampus Middle	brain
16	chr2:72501800-72503200	Enhancers	Brain Germinal Matrix	brain
17	chr2:72502200-72503400	Enhancers	Small Intestine	intestine
18	chr2:72502200-72504200	Enhancers	Rectal Mucosa Donor 31	rectum
19	chr2:72502200-72505400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
20	chr2:72502400-72503000	Enhancers	HepG2	liver
21	chr2:72502400-72503200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr2:72502400-72503600	Enhancers	Ovary	ovary
23	chr2:72502400-72503600	Enhancers	Sigmoid Colon	Sigmoid Colon
24	chr2:72502400-72504200	Enhancers	A549	lung
25	chr2:72502600-72503800	Weak transcription	Duodenum Smooth Muscle	Duodenum
26	chr2:72502800-72503400	Enhancers	Right Atrium	heart
27	chr2:72502800-72505200	Weak transcription	Hela-S3	cervix
28	chr2:72502800-72505800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr2:72502800-72507800	Weak transcription	Brain Cingulate Gyrus	brain
30	chr2:72502800-72507800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links