Variant report

Variant	rs3934784
Chromosome Location	chr2:191448249-191448250
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:191393388..191396315-chr2:191446782..191449171,2	K562	blood:
2	chr2:191446916..191449230-chr2:191454254..191457389,3	K562	blood:
3	chr2:191447673..191449852-chr2:191450664..191453418,2	K562	blood:
4	chr2:191447292..191449336-chr2:191452826..191454451,2	MCF-7	breast:

Extended variants
information (count: 73 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs10204628	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10931455	0.95[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10931459	0.95[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10931460	0.95[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10931464	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11673788	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.88[JPT][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11673921	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11675051	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11677333	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11685221	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11686226	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11891641	0.82[CHB][hapmap];0.88[JPT][hapmap]
rs13005335	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2159821	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2159822	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34101385	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34109383	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34703964	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34751744	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35954637	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4324341	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4343493	0.82[ASW][hapmap];0.86[CEU][hapmap];0.91[TSI][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4384819	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4384820	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4597559	0.82[ASW][hapmap];0.86[CEU][hapmap];0.91[TSI][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4638823	0.82[ASW][hapmap];0.86[CEU][hapmap];0.91[TSI][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs55784091	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs55788736	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55884870	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs55901912	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs55918914	0.80[EUR][1000 genomes]
rs56094872	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs56337518	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs61730953	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61743479	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62181001	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs62181002	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs62181014	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs62181015	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs62181017	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs62181024	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62181026	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62181027	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62181031	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62181032	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62181033	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62181036	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62181053	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62181057	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62182860	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62182861	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62182862	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62182863	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62182864	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62182892	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62182893	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6434404	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6707836	0.80[EUR][1000 genomes]
rs6708018	0.80[EUR][1000 genomes]
rs6714829	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6719656	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6727054	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6742904	0.89[CEU][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6756354	0.83[CEU][hapmap];0.82[CHB][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6757698	0.95[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72905231	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs72905290	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs72907168	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72911128	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7573621	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7574871	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7721	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];0.88[JPT][hapmap];0.86[TSI][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[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	nsv834492	chr2:191438864-191646621	Flanking Bivalent TSS/Enh Active TSS Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs3934784	INPP1	cis	cerebellum	SCAN
rs3934784	ZC3H15	cis	cerebellum	SCAN
rs3934784	FLJ20160	cis	multi-tissue	Pritchard
rs3934784	HIBCH	cis	lymphoblastoid	seeQTL
rs3934784	MFSD6	cis	lymphoblastoid	seeQTL

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:191436800-191457000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr2:191443600-191448400	Weak transcription	Placenta	Placenta
3	chr2:191443800-191448400	Weak transcription	Left Ventricle	heart
4	chr2:191443800-191450200	Weak transcription	Esophagus	oesophagus
5	chr2:191443800-191456600	Weak transcription	Psoas Muscle	Psoas
6	chr2:191444000-191449600	Weak transcription	Fetal Brain Male	brain
7	chr2:191444200-191456800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
8	chr2:191445000-191448400	Weak transcription	Ovary	ovary
9	chr2:191445200-191448400	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr2:191445400-191450800	Enhancers	Fetal Stomach	stomach
11	chr2:191445600-191448400	Weak transcription	Small Intestine	intestine
12	chr2:191445800-191449000	Enhancers	K562	blood
13	chr2:191446600-191448800	Enhancers	Right Atrium	heart
14	chr2:191446600-191449000	Enhancers	Brain Cingulate Gyrus	brain
15	chr2:191446600-191449000	Enhancers	Brain Substantia Nigra	brain
16	chr2:191446600-191449400	Enhancers	Fetal Heart	heart
17	chr2:191446800-191448600	Enhancers	Brain Hippocampus Middle	brain
18	chr2:191446800-191448800	Enhancers	Brain Angular Gyrus	brain
19	chr2:191447000-191448400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
20	chr2:191447000-191448800	Enhancers	Brain Anterior Caudate	brain
21	chr2:191447000-191448800	Enhancers	Brain Inferior Temporal Lobe	brain
22	chr2:191447000-191449200	Enhancers	Fetal Muscle Leg	muscle
23	chr2:191447200-191448800	Enhancers	Colon Smooth Muscle	Colon
24	chr2:191447400-191448600	Enhancers	Muscle Satellite Cultured Cells	--
25	chr2:191447400-191448600	Enhancers	Rectal Smooth Muscle	rectum
26	chr2:191447400-191449000	Enhancers	Hela-S3	cervix
27	chr2:191447600-191448600	Enhancers	A549	lung
28	chr2:191447600-191448800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr2:191447600-191448800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr2:191447600-191449000	Enhancers	Adipose Nuclei	Adipose
31	chr2:191447600-191449200	Enhancers	Primary B cells from peripheral blood	blood
32	chr2:191447600-191451200	Enhancers	NHDF-Ad	bronchial
33	chr2:191447800-191448400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr2:191447800-191448400	Weak transcription	Right Ventricle	heart
35	chr2:191447800-191448400	Enhancers	HepG2	liver
36	chr2:191447800-191449000	Enhancers	Skeletal Muscle Male	skeletal muscle
37	chr2:191448000-191448600	Weak transcription	HSMMtube	muscle
38	chr2:191448000-191448600	Enhancers	NHEK	skin
39	chr2:191448000-191448800	Enhancers	HMEC	breast
40	chr2:191448200-191448400	Enhancers	Skeletal Muscle Female	skeletal muscle
41	chr2:191448200-191448600	Flanking Active TSS	Fetal Lung	lung
42	chr2:191448200-191448600	Enhancers	Osteobl	bone
43	chr2:191448200-191449200	Flanking Active TSS	GM12878-XiMat	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links