Variant report

Variant	rs198609
Chromosome Location	chr13:48978145-48978146
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 80 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs12584784	0.91[ASN][1000 genomes]
rs171988	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs171990	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs174857	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];0.93[YRI][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs198564	0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs198568	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.94[YRI][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs198571	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.93[YRI][hapmap];0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs198574	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.88[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs198575	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.94[YRI][hapmap];0.92[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs198576	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.94[YRI][hapmap];0.92[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs198577	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.93[YRI][hapmap];0.92[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs198606	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.93[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs198608	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs198610	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.94[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs198614	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.93[YRI][hapmap]
rs198622	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.94[YRI][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs198623	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes]
rs198624	0.97[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs198627	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs198629	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs198630	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs198631	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2070752	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2274400	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs2515669	0.80[AFR][1000 genomes]
rs2804094	1.00[CEU][hapmap];0.82[YRI][hapmap];0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2804095	1.00[CHB][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2854342	1.00[CEU][hapmap];0.81[JPT][hapmap];0.93[YRI][hapmap];0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2854348	0.94[YRI][hapmap];0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2854353	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.94[YRI][hapmap];0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2854357	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.94[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2854362	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.94[YRI][hapmap];0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3092888	1.00[CHB][hapmap];0.90[JPT][hapmap];0.91[ASN][1000 genomes]
rs3092899	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[ASN][1000 genomes]
rs3751380	0.88[CHB][hapmap];0.90[JPT][hapmap]
rs398158	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.94[YRI][hapmap];0.99[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs403390	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[JPT][hapmap];0.94[YRI][hapmap];0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs406098	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.93[YRI][hapmap];0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4151441	0.90[ASN][1000 genomes]
rs4151442	1.00[CHB][hapmap];0.81[JPT][hapmap];0.90[ASN][1000 genomes]
rs4151448	1.00[CHB][hapmap];0.81[JPT][hapmap];0.90[ASN][1000 genomes]
rs4151452	1.00[CHB][hapmap];0.90[ASN][1000 genomes]
rs4151456	0.85[CHB][hapmap];0.81[ASN][1000 genomes]
rs4151461	0.81[ASN][1000 genomes]
rs4151474	1.00[CHB][hapmap];0.90[ASN][1000 genomes]
rs4151476	0.90[ASN][1000 genomes]
rs4151525	0.86[CHB][hapmap];0.83[ASN][1000 genomes]
rs4151601	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs425834	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[YRI][hapmap];0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs427686	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.94[YRI][hapmap];0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56871512	0.83[ASN][1000 genomes]
rs58658780	0.90[ASN][1000 genomes]
rs60887299	0.81[ASN][1000 genomes]
rs6561448	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap]
rs6561457	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap]
rs6561461	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap]
rs6561465	1.00[CEU][hapmap]
rs7325962	0.88[CHB][hapmap];0.90[JPT][hapmap];0.88[EUR][1000 genomes]
rs7329865	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs7333985	0.91[ASN][1000 genomes]
rs7335353	0.90[ASN][1000 genomes]
rs73488925	0.90[ASN][1000 genomes]
rs74075993	0.95[ASN][1000 genomes]
rs7983002	0.90[ASN][1000 genomes]
rs7995216	0.88[CHB][hapmap];0.90[JPT][hapmap]
rs7996186	0.86[CHB][hapmap]
rs7998781	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap]
rs8001241	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap]
rs8002565	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap]
rs877664	0.90[ASN][1000 genomes]
rs9316385	0.80[EUR][1000 genomes]
rs9331965	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs9331973	0.86[CHB][hapmap]
rs9332054	0.81[JPT][hapmap]
rs9332278	1.00[CEU][hapmap]
rs9595931	1.00[CEU][hapmap]

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	esv1803998	chr13:48966078-48986320	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
2	nsv1050786	chr13:48971510-48987032	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv1053432	chr13:48971510-48992810	Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv1043486	chr13:48971510-48996995	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:48916800-48985400	Weak transcription	Colonic Mucosa	Colon
2	chr13:48934600-48984200	Weak transcription	Right Ventricle	heart
3	chr13:48943600-48984200	Weak transcription	Brain Angular Gyrus	brain
4	chr13:48944600-48983400	Weak transcription	Psoas Muscle	Psoas
5	chr13:48966400-48986000	Weak transcription	Lung	lung
6	chr13:48966800-48984200	Weak transcription	Placenta	Placenta
7	chr13:48968800-48984200	Weak transcription	Stomach Smooth Muscle	stomach
8	chr13:48969000-48984200	Weak transcription	Fetal Intestine Large	intestine
9	chr13:48969000-48984400	Weak transcription	Cortex derived primary cultured neurospheres	brain
10	chr13:48969200-48984200	Weak transcription	Fetal Stomach	stomach
11	chr13:48969200-48984400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr13:48970600-48984200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr13:48972000-48978800	Enhancers	Breast Myoepithelial Primary Cells	Breast
14	chr13:48972000-48980000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr13:48972600-48982600	Enhancers	Primary T helper cells fromperipheralblood	blood
16	chr13:48973800-48978600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
17	chr13:48973800-48984000	Enhancers	Primary T helper naive cells from peripheral blood	blood
18	chr13:48974400-48979000	Enhancers	Primary hematopoietic stem cells	blood
19	chr13:48974600-48978400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
20	chr13:48974600-48986000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr13:48975200-48978200	Weak transcription	Primary B cells from peripheral blood	blood
22	chr13:48975200-48978600	Weak transcription	Colon Smooth Muscle	Colon
23	chr13:48975200-48979800	Weak transcription	Fetal Heart	heart
24	chr13:48975200-48980600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr13:48975200-48983800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
26	chr13:48975200-48984000	Weak transcription	Rectal Mucosa Donor 31	rectum
27	chr13:48975200-48984200	Weak transcription	Fetal Intestine Small	intestine
28	chr13:48975200-48985400	Weak transcription	Sigmoid Colon	Sigmoid Colon
29	chr13:48975400-48983000	Weak transcription	Brain Hippocampus Middle	brain
30	chr13:48975400-48984200	Weak transcription	Duodenum Mucosa	Duodenum
31	chr13:48975600-48980800	Weak transcription	HSMM	muscle
32	chr13:48975600-48983000	Weak transcription	Rectal Mucosa Donor 29	rectum
33	chr13:48975600-48984000	Weak transcription	Stomach Mucosa	stomach
34	chr13:48975600-48985200	Weak transcription	NH-A	brain
35	chr13:48975800-48980200	Enhancers	Primary hematopoietic stem cells short term culture	blood
36	chr13:48975800-48983000	Weak transcription	Fetal Kidney	kidney
37	chr13:48975800-48984000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
38	chr13:48976000-48984200	Weak transcription	Primary B cells from cord blood	blood
39	chr13:48976000-48984200	Weak transcription	A549	lung
40	chr13:48976000-48984200	Weak transcription	NHLF	lung
41	chr13:48976000-48984400	Weak transcription	HSMMtube	muscle
42	chr13:48976000-49005800	Weak transcription	Hela-S3	cervix
43	chr13:48976400-48978400	Enhancers	Primary T killer memory cells from peripheral blood	blood
44	chr13:48976400-48979200	Enhancers	Primary T cells fromperipheralblood	blood
45	chr13:48976800-48978600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
46	chr13:48976800-48982000	Weak transcription	HepG2	liver
47	chr13:48976800-48983800	Weak transcription	Ovary	ovary
48	chr13:48977000-48978400	Enhancers	GM12878-XiMat	blood
49	chr13:48977000-48984000	Weak transcription	Liver	Liver
50	chr13:48977000-48984000	Weak transcription	HUVEC	blood vessel

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links