Variant report

Variant	rs2566876
Chromosome Location	chr7:128890055-128890056
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 66 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs1000676	0.81[JPT][hapmap]
rs10248810	0.95[CEU][hapmap];0.86[JPT][hapmap];0.81[EUR][1000 genomes]
rs10257620	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10954224	0.85[ASN][1000 genomes]
rs10954226	0.87[CEU][hapmap];0.91[GIH][hapmap];0.86[JPT][hapmap];0.85[TSI][hapmap]
rs10954230	0.81[JPT][hapmap]
rs11769045	0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11979476	0.82[CEU][hapmap];0.91[GIH][hapmap];0.86[JPT][hapmap];0.90[TSI][hapmap]
rs12111832	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12112374	0.82[CEU][hapmap];0.91[GIH][hapmap];0.86[JPT][hapmap];0.87[TSI][hapmap]
rs12216567	0.92[AFR][1000 genomes];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12534372	0.81[JPT][hapmap]
rs12540568	0.81[JPT][hapmap]
rs12667132	0.81[JPT][hapmap]
rs13226649	0.91[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs13235668	0.85[ASN][1000 genomes]
rs13235749	0.85[ASN][1000 genomes]
rs1473236	0.84[ASN][1000 genomes]
rs1526900	0.86[JPT][hapmap];0.83[MEX][hapmap]
rs1559486	0.91[JPT][hapmap]
rs1880854	0.87[ASW][hapmap];1.00[CEU][hapmap];0.91[GIH][hapmap];0.86[JPT][hapmap];0.98[LWK][hapmap];0.96[MEX][hapmap];0.96[MKK][hapmap];0.95[TSI][hapmap];0.93[YRI][hapmap];0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2012919	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2141075	0.84[ASN][1000 genomes]
rs2402944	0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2566877	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2566885	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2566886	0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2694572	0.87[ASW][hapmap];0.95[CEU][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2694574	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2718083	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap]
rs2718084	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.83[MEX][hapmap];0.89[MKK][hapmap];0.92[TSI][hapmap];0.86[YRI][hapmap];0.88[AFR][1000 genomes];0.80[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2718089	0.96[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2718093	0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2718096	0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2718115	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2896415	0.84[ASN][1000 genomes]
rs4728163	0.81[JPT][hapmap]
rs4728164	0.81[JPT][hapmap]
rs4731566	0.85[ASN][1000 genomes]
rs4731572	0.81[JPT][hapmap]
rs55638303	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62480596	0.81[ASN][1000 genomes]
rs6467233	0.87[CEU][hapmap];0.82[CHB][hapmap];0.88[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.83[ASN][1000 genomes]
rs6467237	0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6467240	0.83[EUR][1000 genomes]
rs66970518	0.83[ASN][1000 genomes]
rs67820265	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67853067	0.82[ASN][1000 genomes]
rs68184415	0.82[EUR][1000 genomes]
rs6942756	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6966595	0.82[CEU][hapmap];0.91[GIH][hapmap];0.91[JPT][hapmap];0.81[LWK][hapmap];0.89[MKK][hapmap]
rs6967464	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6980385	0.82[CEU][hapmap];0.91[GIH][hapmap];0.86[JPT][hapmap];0.90[TSI][hapmap]
rs7780886	0.85[ASN][1000 genomes]
rs7782348	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7788327	0.95[CEU][hapmap];0.86[GIH][hapmap];0.86[JPT][hapmap];0.89[LWK][hapmap];0.96[MEX][hapmap];0.93[MKK][hapmap];0.97[TSI][hapmap];0.82[EUR][1000 genomes]
rs7794622	0.81[EUR][1000 genomes]
rs822038	0.82[CEU][hapmap];0.91[JPT][hapmap]
rs822040	0.82[CEU][hapmap];0.91[JPT][hapmap]
rs891545	0.87[ASW][hapmap];1.00[CEU][hapmap];0.88[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.96[MEX][hapmap];0.98[MKK][hapmap];0.95[TSI][hapmap];0.93[YRI][hapmap];0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs963465	1.00[CEU][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9640854	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9641846	0.87[ASW][hapmap];1.00[CEU][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.95[TSI][hapmap];0.93[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9641849	0.97[ASN][1000 genomes]

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	nsv1031284	chr7:128866118-128910506	Enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	esv3349195	chr7:128887559-128918489	Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2566876	LOC407835	cis	cerebellum	SCAN
rs2566876	COPG2	cis	cerebellum	SCAN
rs2566876	KCP	cis	cerebellum	SCAN

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:128866000-128902200	Weak transcription	Gastric	stomach
2	chr7:128866200-128898600	Weak transcription	Thymus	Thymus
3	chr7:128866400-128891400	Weak transcription	Fetal Stomach	stomach
4	chr7:128866400-128899000	Weak transcription	Ovary	ovary
5	chr7:128866600-128901400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr7:128867000-128898400	Weak transcription	Primary T helper cells PMA-I stimulated	--
7	chr7:128867200-128909800	Weak transcription	Primary B cells from cord blood	blood
8	chr7:128868600-128897200	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr7:128872800-128892000	Weak transcription	Skeletal Muscle Female	skeletal muscle
10	chr7:128878800-128897000	Weak transcription	Monocytes-CD14+_RO01746	blood
11	chr7:128881000-128892000	Weak transcription	Brain Cingulate Gyrus	brain
12	chr7:128881000-128898800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr7:128882000-128899600	Weak transcription	Left Ventricle	heart
14	chr7:128884800-128898800	Weak transcription	Primary T cells from cord blood	blood
15	chr7:128885600-128898600	Weak transcription	Brain Germinal Matrix	brain
16	chr7:128887200-128898600	Weak transcription	NHEK	skin
17	chr7:128887600-128892400	Weak transcription	Pancreas	Pancrea
18	chr7:128888000-128891800	Weak transcription	Brain Anterior Caudate	brain
19	chr7:128888200-128895800	Weak transcription	HUES48 Cell Line	embryonic stem cell
20	chr7:128889800-128890200	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr7:128889800-128890200	ZNF genes & repeats	Fetal Intestine Small	intestine
22	chr7:128890000-128890200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell

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