Variant report

Variant	rs4855852
Chromosome Location	chr3:49649071-49649072
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 92 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:91)

rs_ID	r²[population]
rs1050088	0.85[CHD][hapmap];0.97[GIH][hapmap];0.86[JPT][hapmap];0.83[MEX][hapmap]
rs1060962	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10640	0.88[GIH][hapmap];0.86[JPT][hapmap]
rs10865955	0.86[CHD][hapmap];0.97[GIH][hapmap];0.86[JPT][hapmap];0.83[MEX][hapmap]
rs11130192	1.00[JPT][hapmap]
rs11130199	0.86[CHD][hapmap];0.94[GIH][hapmap];0.86[JPT][hapmap];0.83[MEX][hapmap]
rs11130212	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11130213	0.92[CHD][hapmap];0.85[GIH][hapmap]
rs1131095	0.92[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs11709525	0.92[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs11710037	0.87[ASN][1000 genomes]
rs11711485	0.88[GIH][hapmap];0.86[JPT][hapmap]
rs11715915	0.88[GIH][hapmap];0.86[JPT][hapmap]
rs11718165	0.92[CHD][hapmap];0.85[GIH][hapmap]
rs11720264	0.86[JPT][hapmap]
rs11917431	0.92[ASN][1000 genomes]
rs11919311	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11921590	0.92[ASN][1000 genomes]
rs11922013	0.82[JPT][hapmap]
rs12489092	0.86[JPT][hapmap]
rs12490267	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12497288	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13085791	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs13316695	0.87[ASN][1000 genomes]
rs1352890	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1464566	0.86[CHD][hapmap];0.97[GIH][hapmap];0.86[JPT][hapmap];0.83[MEX][hapmap]
rs1464567	0.85[CHD][hapmap];0.97[GIH][hapmap];0.86[JPT][hapmap]
rs1464568	0.86[CHD][hapmap];0.97[GIH][hapmap];0.86[JPT][hapmap];0.83[MEX][hapmap]
rs1568661	0.86[CHD][hapmap];0.97[GIH][hapmap];0.86[JPT][hapmap]
rs1801143	0.88[GIH][hapmap];0.86[JPT][hapmap]
rs1826347	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap]
rs1873625	0.92[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs1873626	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2005557	1.00[CEU][hapmap];0.80[YRI][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2131104	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.80[YRI][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2131109	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2172252	1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs2329020	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.98[TSI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2960548	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3197999	0.92[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs34762726	0.92[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs35007338	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35404120	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35701831	0.97[GIH][hapmap];0.86[JPT][hapmap];0.83[MEX][hapmap]
rs3811697	0.88[GIH][hapmap];0.86[JPT][hapmap]
rs3870338	0.86[CHD][hapmap];0.97[GIH][hapmap];0.86[JPT][hapmap];0.83[MEX][hapmap]
rs3924462	0.86[CHD][hapmap];0.97[GIH][hapmap];0.86[JPT][hapmap];0.83[MEX][hapmap];0.89[MKK][hapmap]
rs4283605	0.92[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs4625	0.88[GIH][hapmap];0.86[JPT][hapmap]
rs4855835	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4855839	0.85[CHD][hapmap];0.91[GIH][hapmap];0.86[JPT][hapmap];0.86[MEX][hapmap]
rs4855847	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4855859	0.86[CHD][hapmap];0.97[GIH][hapmap];0.86[JPT][hapmap];0.87[MEX][hapmap];0.89[MKK][hapmap]
rs4855864	0.86[CHD][hapmap];0.97[GIH][hapmap];0.86[JPT][hapmap];0.83[MEX][hapmap]
rs4855873	0.86[CHD][hapmap];0.97[GIH][hapmap];0.86[JPT][hapmap];0.83[MEX][hapmap]
rs4855881	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.96[YRI][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4855883	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4855884	1.00[CEU][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6446272	0.88[GIH][hapmap];0.86[JPT][hapmap]
rs6765869	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6766131	0.88[GIH][hapmap];0.86[JPT][hapmap]
rs6767878	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6770670	1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs6779524	0.88[GIH][hapmap];0.86[JPT][hapmap]
rs6782577	0.96[CEU][hapmap]
rs6784820	0.86[CHD][hapmap];0.97[GIH][hapmap];0.86[JPT][hapmap];0.83[MEX][hapmap];0.89[MKK][hapmap]
rs6803222	0.92[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs6997	0.88[GIH][hapmap];0.86[JPT][hapmap]
rs7614725	0.92[ASN][1000 genomes]
rs7622302	0.88[GIH][hapmap];0.86[JPT][hapmap]
rs7633271	0.86[JPT][hapmap]
rs7637999	0.86[CHD][hapmap];0.97[GIH][hapmap];0.86[JPT][hapmap];0.83[MEX][hapmap];0.89[MKK][hapmap]
rs7646366	0.88[GIH][hapmap];0.86[JPT][hapmap]
rs885592	0.86[CHD][hapmap];0.97[GIH][hapmap];0.86[JPT][hapmap];0.83[MEX][hapmap];0.89[MKK][hapmap]
rs9812791	0.92[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs9814873	0.88[GIH][hapmap];0.86[JPT][hapmap]
rs9822268	0.92[CHD][hapmap];0.85[GIH][hapmap];0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs9824092	0.87[ASN][1000 genomes]
rs9827021	0.86[JPT][hapmap]
rs9827708	0.92[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs9833611	0.92[ASN][1000 genomes]
rs9837027	0.88[GIH][hapmap];0.86[JPT][hapmap]
rs9837341	1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs9837520	0.82[ASN][1000 genomes]
rs9841110	0.86[JPT][hapmap]
rs9853683	0.88[GIH][hapmap];0.86[JPT][hapmap]
rs9858280	0.88[GIH][hapmap];0.86[JPT][hapmap]
rs9858542	0.92[CHD][hapmap];0.85[GIH][hapmap]
rs9862080	0.87[ASN][1000 genomes]
rs9875617	0.88[GIH][hapmap];0.86[JPT][hapmap]
rs9882740	0.92[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv508217	chr3:49615446-49769896	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs4855852	CACNA2D2	cis	cerebellum	SCAN
rs4855852	SLC6A20	cis	cerebellum	SCAN
rs4855852	CISH	cis	lymphoblastoid	seeQTL
rs4855852	ALS2CL	cis	cerebellum	SCAN
rs4855852	IP6K2	cis	cerebellum	SCAN
rs4855852	ARIH2	cis	parietal	SCAN
rs4855852	CISH	cis	parietal	SCAN
rs4855852	CCDC71	cis	cerebellum	SCAN

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49637800-49653600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr3:49641200-49653600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr3:49645800-49653600	Weak transcription	Fetal Lung	lung
4	chr3:49646600-49649200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
5	chr3:49646800-49649400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr3:49647000-49649400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr3:49647000-49649600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr3:49647400-49653400	Weak transcription	Fetal Brain Female	brain
9	chr3:49647800-49653000	Weak transcription	Fetal Heart	heart
10	chr3:49648000-49649400	Enhancers	HepG2	liver
11	chr3:49648200-49649400	Enhancers	Fetal Muscle Leg	muscle
12	chr3:49648400-49662000	Weak transcription	Brain Germinal Matrix	brain
13	chr3:49648600-49653800	Weak transcription	NHDF-Ad	bronchial
14	chr3:49648600-49654000	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr3:49648800-49649400	Enhancers	Fetal Muscle Trunk	muscle
16	chr3:49648800-49652000	Weak transcription	Brain Angular Gyrus	brain
17	chr3:49648800-49653600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin

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