Variant report

Variant	rs10490468
Chromosome Location	chr2:53964506-53964507
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 69 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs11897282	0.92[CHB][hapmap];0.96[CHD][hapmap];0.90[JPT][hapmap];0.83[MKK][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs11901698	0.92[CHB][hapmap];0.91[YRI][hapmap]
rs1232	0.92[CHB][hapmap];0.83[GIH][hapmap];0.81[JPT][hapmap];0.84[MEX][hapmap];0.84[ASN][1000 genomes]
rs13408029	1.00[CHB][hapmap];0.81[JPT][hapmap];0.88[ASN][1000 genomes]
rs17045176	0.92[CHB][hapmap];0.90[JPT][hapmap];0.96[ASN][1000 genomes]
rs17045199	0.83[CEU][hapmap];0.86[MEX][hapmap]
rs17045203	0.92[CHB][hapmap];0.88[CHD][hapmap]
rs17520505	1.00[CHB][hapmap];0.81[JPT][hapmap];0.91[YRI][hapmap];0.87[ASN][1000 genomes]
rs17521008	0.83[CHD][hapmap];0.87[MKK][hapmap];0.92[ASN][1000 genomes]
rs2008082	0.82[ASN][1000 genomes]
rs2287340	0.92[CHB][hapmap];0.92[CHD][hapmap];0.83[ASN][1000 genomes]
rs2302797	0.92[CHB][hapmap];0.96[CHD][hapmap];0.90[JPT][hapmap];0.88[MKK][hapmap];0.93[ASN][1000 genomes]
rs2542572	0.90[CHB][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs2542573	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2542580	0.84[ASN][1000 genomes]
rs2542581	0.83[MKK][hapmap];1.00[YRI][hapmap]
rs2542582	0.82[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.97[TSI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2542583	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2542589	0.92[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2542590	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2542591	0.87[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2542592	0.87[CEU][hapmap];0.92[CHB][hapmap];0.90[JPT][hapmap];0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2543629	0.84[CHB][hapmap];0.86[CHD][hapmap];0.86[ASN][1000 genomes]
rs2692512	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2692513	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2692516	0.80[MEX][hapmap]
rs2692519	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.97[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2692521	0.86[ASN][1000 genomes]
rs2692522	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2692530	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2692533	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2692534	0.88[CEU][hapmap];0.86[MEX][hapmap]
rs2909262	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2949813	0.84[CHB][hapmap];0.81[JPT][hapmap];0.83[YRI][hapmap];0.84[ASN][1000 genomes]
rs2949814	0.82[ASN][1000 genomes]
rs35772199	0.87[ASN][1000 genomes]
rs3731970	0.83[YRI][hapmap]
rs3770394	0.92[CHB][hapmap];0.90[JPT][hapmap];0.93[ASN][1000 genomes]
rs3770395	0.93[ASN][1000 genomes]
rs3770397	0.96[ASN][1000 genomes]
rs3770399	0.93[ASN][1000 genomes]
rs3770407	0.83[YRI][hapmap]
rs3770411	0.84[CHB][hapmap];0.88[CHD][hapmap];0.83[YRI][hapmap];0.83[ASN][1000 genomes]
rs4116709	1.00[CHB][hapmap];0.81[JPT][hapmap];0.87[ASN][1000 genomes]
rs55897904	0.84[ASN][1000 genomes]
rs56214822	0.82[ASN][1000 genomes]
rs58326257	0.84[ASN][1000 genomes]
rs62137573	0.92[ASN][1000 genomes]
rs62137602	0.96[ASN][1000 genomes]
rs62137605	0.82[ASN][1000 genomes]
rs62137606	0.91[ASN][1000 genomes]
rs62137610	0.87[ASN][1000 genomes]
rs62137611	0.87[ASN][1000 genomes]
rs6730006	0.91[ASN][1000 genomes]
rs719127	0.92[CHB][hapmap];0.81[JPT][hapmap];1.00[YRI][hapmap];0.88[ASN][1000 genomes]
rs72901256	0.92[ASN][1000 genomes]
rs7558968	0.82[ASN][1000 genomes]
rs7600817	0.93[ASN][1000 genomes]
rs805316	0.83[ASW][hapmap];0.92[CHB][hapmap];0.81[JPT][hapmap];0.85[MEX][hapmap]
rs805368	0.83[ASN][1000 genomes]
rs805383	0.84[ASN][1000 genomes]
rs805385	0.84[ASN][1000 genomes]
rs805398	0.81[ASN][1000 genomes]
rs805435	0.84[ASN][1000 genomes]
rs805437	0.92[ASW][hapmap];0.87[CEU][hapmap];0.92[CHB][hapmap];0.97[GIH][hapmap];0.81[JPT][hapmap];0.91[TSI][hapmap];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003263	chr2:53863287-54055359	Strong transcription Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
2	nsv535720	chr2:53863287-54055359	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
3	nsv834058	chr2:53900674-54072011	Strong transcription Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
4	esv1844655	chr2:53929855-53972693	Strong transcription ZNF genes & repeats Weak transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10490468	PSME4	cis	lymphoblastoid	seeQTL
rs10490468	ACYP2	cis	Muscle Skeletal	GTEx
rs10490468	ACYP2	cis	multi-tissue	Pritchard

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:53908600-53982200	Weak transcription	Small Intestine	intestine
2	chr2:53910000-53994000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
3	chr2:53910200-53990600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
4	chr2:53918400-53994000	Weak transcription	Fetal Heart	heart
5	chr2:53925400-53979400	Weak transcription	Psoas Muscle	Psoas
6	chr2:53936600-53968400	Weak transcription	Pancreas	Pancrea
7	chr2:53936600-53978600	Weak transcription	Hela-S3	cervix
8	chr2:53936800-53985400	Weak transcription	Stomach Smooth Muscle	stomach
9	chr2:53937000-53983800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr2:53937000-53994400	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr2:53937200-53966800	Weak transcription	Gastric	stomach
12	chr2:53937200-53978600	Weak transcription	NH-A	brain
13	chr2:53937200-53983600	Weak transcription	Right Ventricle	heart
14	chr2:53937200-53994200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr2:53937400-53979600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr2:53937400-53990200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
17	chr2:53937400-53994400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
18	chr2:53938000-53974800	Weak transcription	H1 Cell Line	embryonic stem cell
19	chr2:53938000-53974800	Weak transcription	Placenta	Placenta
20	chr2:53938200-53967000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr2:53938200-53975200	Weak transcription	Duodenum Mucosa	Duodenum
22	chr2:53938400-53969400	Weak transcription	Rectal Smooth Muscle	rectum
23	chr2:53938400-53969600	Weak transcription	Esophagus	oesophagus
24	chr2:53938400-53975000	Weak transcription	Fetal Kidney	kidney
25	chr2:53938400-53982800	Weak transcription	HUES48 Cell Line	embryonic stem cell
26	chr2:53938400-53983400	Weak transcription	HSMMtube	muscle
27	chr2:53938400-53992400	Weak transcription	K562	blood
28	chr2:53938600-53972000	Weak transcription	HSMM	muscle
29	chr2:53941800-53974400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
30	chr2:53941800-53976400	Weak transcription	Colon Smooth Muscle	Colon
31	chr2:53943800-53974800	Weak transcription	Rectal Mucosa Donor 29	rectum
32	chr2:53943800-53983600	Weak transcription	Ovary	ovary
33	chr2:53943800-53983600	Weak transcription	Thymus	Thymus
34	chr2:53943800-53983800	Weak transcription	Left Ventricle	heart
35	chr2:53944000-53974600	Weak transcription	Duodenum Smooth Muscle	Duodenum
36	chr2:53945800-53968400	Weak transcription	Brain Anterior Caudate	brain
37	chr2:53949800-53974200	Weak transcription	HUES64 Cell Line	embryonic stem cell
38	chr2:53952200-53978600	Weak transcription	Osteobl	bone
39	chr2:53952400-53983600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
40	chr2:53952600-53974800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr2:53954400-53972000	Weak transcription	NHDF-Ad	bronchial
42	chr2:53954800-53969600	Weak transcription	Muscle Satellite Cultured Cells	--
43	chr2:53954800-53982000	Weak transcription	Sigmoid Colon	Sigmoid Colon
44	chr2:53954800-53983800	Weak transcription	Lung	lung
45	chr2:53955400-53965800	Weak transcription	Primary neutrophils fromperipheralblood	blood
46	chr2:53955800-53974600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
47	chr2:53956000-53979600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
48	chr2:53956000-53983400	Weak transcription	Fetal Brain Male	brain
49	chr2:53956200-53983000	Weak transcription	Fetal Muscle Leg	muscle
50	chr2:53956800-53967800	Weak transcription	Brain Substantia Nigra	brain

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