Variant report

Variant	rs10204415
Chromosome Location	chr2:72507640-72507641
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 168 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:166)

rs_ID	r²[population]
rs1000523	0.87[CEU][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10168145	1.00[CHB][hapmap]
rs10173381	1.00[CHB][hapmap]
rs10175915	0.87[CEU][hapmap];0.95[GIH][hapmap];0.87[MEX][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10178138	0.87[CEU][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10178847	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10181899	0.87[CEU][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10186080	1.00[CHB][hapmap]
rs10190674	1.00[CHB][hapmap]
rs10192800	1.00[CHB][hapmap]
rs10193543	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10203965	1.00[CHB][hapmap]
rs10205108	0.91[GIH][hapmap]
rs10207299	1.00[CHB][hapmap]
rs10221767	0.87[CEU][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10221769	0.91[GIH][hapmap]
rs11126366	1.00[CHB][hapmap]
rs1123199	0.87[CEU][hapmap];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1159764	0.91[GIH][hapmap]
rs1159766	0.91[GIH][hapmap]
rs11690734	1.00[CHB][hapmap]
rs11694921	1.00[CHB][hapmap]
rs11902025	1.00[CHB][hapmap]
rs12463825	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12466026	0.87[CEU][hapmap];0.87[EUR][1000 genomes]
rs12466112	0.87[CEU][hapmap];0.87[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	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13383535	1.00[CHB][hapmap]
rs13387630	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13389524	0.87[CEU][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13390754	1.00[CHB][hapmap]
rs13392314	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13409513	1.00[CHB][hapmap]
rs13409641	0.93[CEU][hapmap];1.00[CHB][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13417114	0.87[GIH][hapmap]
rs13430254	0.87[CEU][hapmap];0.88[EUR][1000 genomes]
rs13430651	0.88[EUR][1000 genomes]
rs13432350	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap]
rs1400582	1.00[CHB][hapmap]
rs1568145	1.00[CHB][hapmap]
rs17673916	0.87[CEU][hapmap];0.91[GIH][hapmap];0.87[MEX][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17724205	0.87[CEU][hapmap];0.87[EUR][1000 genomes]
rs17724860	0.87[CEU][hapmap];0.95[GIH][hapmap];0.87[MEX][hapmap];0.83[TSI][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17725024	0.87[CEU][hapmap];0.95[GIH][hapmap];0.87[MEX][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs194235	0.83[GIH][hapmap]
rs2041563	0.83[GIH][hapmap]
rs2080044	0.87[CEU][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2109960	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs2109963	0.83[GIH][hapmap]
rs2159823	0.87[CEU][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2192014	1.00[CHB][hapmap]
rs2192015	1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap]
rs2203679	1.00[CHB][hapmap]
rs2420444	1.00[CHB][hapmap]
rs2901146	1.00[CHB][hapmap]
rs3115351	1.00[CHB][hapmap]
rs41386	0.95[GIH][hapmap]
rs41388	0.91[GIH][hapmap]
rs41389	0.91[GIH][hapmap]
rs41393	0.91[GIH][hapmap]
rs41394	0.91[GIH][hapmap]
rs41398	0.87[GIH][hapmap]
rs41401	0.83[GIH][hapmap]
rs41402	0.83[GIH][hapmap]
rs41403	0.91[GIH][hapmap]
rs41407	0.91[GIH][hapmap]
rs41412	0.87[GIH][hapmap]
rs41415	0.91[GIH][hapmap];0.81[MEX][hapmap]
rs41416	0.91[GIH][hapmap];0.81[MEX][hapmap]
rs41417	0.95[GIH][hapmap];0.81[MEX][hapmap]
rs4852286	1.00[CHB][hapmap];0.95[GIH][hapmap];0.87[MEX][hapmap];0.85[TSI][hapmap]
rs4852287	1.00[CHB][hapmap]
rs4852288	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap]
rs4852859	0.88[EUR][1000 genomes]
rs55764675	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs55970539	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs56045434	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs56143801	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs56299443	0.80[AMR][1000 genomes];0.90[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	0.87[EUR][1000 genomes]
rs62147589	0.88[EUR][1000 genomes]
rs62147626	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs62147629	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62147636	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62149273	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs625434	1.00[CHB][hapmap]
rs628432	1.00[CHB][hapmap]
rs630241	1.00[CHB][hapmap]
rs632670	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]
rs6546753	0.83[GIH][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]
rs6709114	1.00[ASN][1000 genomes]
rs6711257	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs671721	1.00[CHB][hapmap]
rs6719255	0.81[MEX][hapmap];0.93[AMR][1000 genomes];0.92[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]
rs6760895	0.83[GIH][hapmap]
rs678684	1.00[CHB][hapmap]
rs680380	1.00[CHB][hapmap]
rs680495	1.00[CHB][hapmap]
rs681574	1.00[CHB][hapmap]
rs684673	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	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7558686	1.00[CHB][hapmap]
rs7558919	1.00[CHB][hapmap]
rs7559131	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap]
rs7565922	0.83[GIH][hapmap]
rs7568803	1.00[CHB][hapmap]
rs7577877	1.00[CHB][hapmap]
rs7583271	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs10204415	FBXO48	cis	cerebellum	SCAN
rs10204415	CCT7	cis	parietal	SCAN
rs10204415	BOLA3	cis	parietal	SCAN
rs10204415	CYP26B1	cis	Whole Blood	GTEx
rs10204415	CCT7	cis	cerebellum	SCAN

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:72489200-72508200	Weak transcription	Aorta	Aorta
2	chr2:72499400-72507800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr2:72499400-72507800	Weak transcription	Psoas Muscle	Psoas
4	chr2:72499600-72510400	Weak transcription	Right Ventricle	heart
5	chr2:72502800-72507800	Weak transcription	Brain Cingulate Gyrus	brain
6	chr2:72502800-72507800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr2:72504200-72508000	Weak transcription	Ovary	ovary
8	chr2:72504800-72513200	Weak transcription	Left Ventricle	heart
9	chr2:72505800-72509800	Weak transcription	A549	lung
10	chr2:72506800-72508400	Enhancers	Fetal Heart	heart
11	chr2:72507600-72508200	Enhancers	iPS-18 Cell Line	embryonic stem cell
12	chr2:72507600-72508200	Enhancers	iPS-20b Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links