Variant report

Variant	rs1478895
Chromosome Location	chr8:11353335-11353336
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 53 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs13256690	0.91[ASN][1000 genomes]
rs13277113	0.83[CHB][hapmap];0.90[CHD][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs1382568	0.87[ASN][1000 genomes]
rs1478887	0.81[ASN][1000 genomes]
rs1478900	0.92[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.90[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1478901	0.83[CHB][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs1531577	0.92[ASN][1000 genomes]
rs1564267	0.85[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.86[GIH][hapmap];0.86[JPT][hapmap];0.90[TSI][hapmap];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17153385	0.85[MEX][hapmap]
rs2061831	0.83[ASN][1000 genomes]
rs2244234	1.00[CEU][hapmap];0.94[CHB][hapmap];0.91[YRI][hapmap];0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2250412	1.00[CEU][hapmap];0.88[CHB][hapmap];0.85[JPT][hapmap];0.84[YRI][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2250788	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2251056	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2254546	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2254660	0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2254891	0.87[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs2409780	0.81[ASN][1000 genomes]
rs2618444	0.81[ASN][1000 genomes]
rs2618455	0.82[CHB][hapmap];0.85[MEX][hapmap]
rs2618456	0.82[CHB][hapmap]
rs2618457	0.81[CHB][hapmap]
rs2618473	0.85[ASN][1000 genomes]
rs2618476	0.94[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs2618478	0.94[CHB][hapmap];0.95[CHD][hapmap];0.90[GIH][hapmap];0.95[JPT][hapmap];0.85[MEX][hapmap];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2618479	0.83[ASW][hapmap];0.94[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.84[LWK][hapmap];0.85[MEX][hapmap];0.83[MKK][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2618480	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2618481	0.94[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs2736332	0.83[ASN][1000 genomes]
rs2736335	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2736340	0.85[ASN][1000 genomes]
rs2736343	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2736344	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2736345	0.94[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2736353	0.81[CHB][hapmap]
rs2736354	0.81[CHB][hapmap];0.85[MEX][hapmap]
rs2736355	0.81[CHB][hapmap]
rs35393613	0.88[ASN][1000 genomes]
rs4840565	0.95[ASN][1000 genomes]
rs4840568	0.83[CHB][hapmap];0.90[CHD][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs62489069	0.88[ASN][1000 genomes]
rs6993775	0.81[CHB][hapmap]
rs7812879	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs922483	0.89[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs9693589	0.83[ASN][1000 genomes]
rs9694294	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.84[YRI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs998682	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs998683	0.83[CHB][hapmap];0.92[CHD][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1035072	chr8:10819444-11480692	Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv539473	chr8:10819444-11480692	Weak transcription Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
3	nsv529399	chr8:10970091-11805960	Enhancers Strong transcription Weak transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
4	esv34097	chr8:11177372-11489894	Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
5	nsv1022074	chr8:11292256-11394526	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Weak transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1478895	FLJ10661	cis	cerebellum	SCAN
rs1478895	FAM167A	cis	lymphoblastoid	seeQTL
rs1478895	C8orf79	cis	cerebellum	SCAN
rs1478895	C8orf13	cis	multi-tissue	Pritchard

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:11339000-11353800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr8:11344200-11353800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr8:11349600-11354400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
4	chr8:11349800-11354000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr8:11350200-11356600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr8:11350400-11354200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
7	chr8:11350400-11354400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
8	chr8:11350400-11355400	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr8:11350600-11354200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
10	chr8:11350800-11353800	Weak transcription	NHDF-Ad	bronchial
11	chr8:11351000-11354800	Weak transcription	Primary hematopoietic stem cells	blood
12	chr8:11351800-11353400	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
13	chr8:11352000-11353800	Active TSS	GM12878-XiMat	blood
14	chr8:11352200-11353400	Flanking Active TSS	Primary B cells from cord blood	blood
15	chr8:11352200-11353800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr8:11352200-11354800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr8:11352200-11360400	Weak transcription	Spleen	Spleen
18	chr8:11352400-11354800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
19	chr8:11352600-11353800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr8:11352600-11353800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr8:11352600-11354800	Enhancers	Osteobl	bone
22	chr8:11352600-11356200	Flanking Active TSS	Dnd41	blood
23	chr8:11352800-11353400	Enhancers	Primary T helper naive cells from peripheral blood	blood
24	chr8:11352800-11354000	Weak transcription	Primary T cells fromperipheralblood	blood
25	chr8:11352800-11354600	Transcr. at gene 5' and 3'	Primary B cells from peripheral blood	blood
26	chr8:11352800-11357600	Enhancers	Primary T helper cells fromperipheralblood	blood
27	chr8:11353000-11353400	Active TSS	Fetal Thymus	thymus
28	chr8:11353000-11353400	Weak transcription	NH-A	brain
29	chr8:11353000-11354400	Weak transcription	Primary T cells from cord blood	blood
30	chr8:11353000-11354400	Weak transcription	Primary T helper cells PMA-I stimulated	--
31	chr8:11353200-11361000	Weak transcription	Rectal Mucosa Donor 29	rectum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links