Variant report

Variant	rs6561448
Chromosome Location	chr13:49084326-49084327
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:49081743..49084542-chr13:49085954..49089235,3	K562	blood:

Extended variants
information (count: 81 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs1547660	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs174857	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap]
rs1926595	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1926596	0.91[ASN][1000 genomes]
rs1926597	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs198564	0.85[ASN][1000 genomes]
rs198568	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs198571	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs198574	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs198575	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs198576	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs198577	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs198606	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs198609	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap]
rs198610	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs198614	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs198622	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2274400	0.88[CHB][hapmap];0.90[JPT][hapmap];0.91[ASN][1000 genomes]
rs2804094	1.00[CEU][hapmap];0.91[JPT][hapmap];0.80[EUR][1000 genomes]
rs2804095	1.00[CHB][hapmap];0.91[JPT][hapmap]
rs28414460	0.91[ASN][1000 genomes]
rs2854342	1.00[CEU][hapmap];0.90[JPT][hapmap];0.80[EUR][1000 genomes]
rs2854348	0.91[JPT][hapmap];0.80[EUR][1000 genomes]
rs2854353	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2854357	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2854362	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs28646083	0.91[ASN][1000 genomes]
rs28674973	0.84[ASN][1000 genomes]
rs2897587	0.81[AFR][1000 genomes]
rs3092888	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3092898	0.88[ASN][1000 genomes]
rs3092899	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap]
rs3751380	0.89[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs398158	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs403390	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs406098	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4151434	0.91[JPT][hapmap]
rs4151442	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs4151448	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs4151452	1.00[CHB][hapmap];0.91[JPT][hapmap]
rs4151456	0.86[CHB][hapmap];0.80[JPT][hapmap]
rs4151474	1.00[CHB][hapmap];0.91[JPT][hapmap]
rs4151525	0.88[CHB][hapmap];0.90[JPT][hapmap]
rs4151601	0.88[CHB][hapmap];0.90[JPT][hapmap]
rs425834	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs427686	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs449268	0.83[AMR][1000 genomes]
rs61074776	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6561457	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6561461	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6561465	1.00[CEU][hapmap]
rs7325962	0.89[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7326934	0.95[YRI][hapmap];0.86[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs7329039	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7329865	0.88[CHB][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs73486867	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73495016	0.88[ASN][1000 genomes]
rs7985825	0.92[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7987935	0.91[ASN][1000 genomes]
rs7992129	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7995216	0.89[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs7996186	0.88[CHB][hapmap];0.90[JPT][hapmap];0.91[ASN][1000 genomes]
rs7996402	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7998781	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.90[AFR][1000 genomes];0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs8001241	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8002565	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9316385	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9316386	0.83[AMR][1000 genomes]
rs9316401	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9331959	0.91[ASN][1000 genomes]
rs9331965	0.88[CHB][hapmap];0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs9331973	0.88[CHB][hapmap];0.90[JPT][hapmap];0.91[ASN][1000 genomes]
rs9332054	0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs9591172	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9591177	0.92[AFR][1000 genomes];0.81[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs9591178	0.92[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
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	nsv832602	chr13:49003159-49167781	Active TSS Enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	nsv1041275	chr13:49045566-49242357	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
3	nsv541769	chr13:49045566-49242357	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Genic enhancers Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
4	nsv832604	chr13:49061081-49281807	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:49054000-49094000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr13:49063000-49087800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr13:49067200-49105200	Weak transcription	Duodenum Smooth Muscle	Duodenum
4	chr13:49067200-49105400	Weak transcription	Rectal Smooth Muscle	rectum
5	chr13:49067800-49098000	Weak transcription	Right Ventricle	heart
6	chr13:49068000-49105600	Weak transcription	Gastric	stomach
7	chr13:49068200-49102600	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr13:49071200-49105600	Weak transcription	Fetal Brain Male	brain
9	chr13:49071800-49086200	Strong transcription	Fetal Stomach	stomach
10	chr13:49071800-49105800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
11	chr13:49072000-49088400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
12	chr13:49072200-49085800	Weak transcription	HUES64 Cell Line	embryonic stem cell
13	chr13:49072200-49095600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr13:49073200-49085800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr13:49073600-49087800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr13:49075400-49085800	Weak transcription	Stomach Smooth Muscle	stomach
17	chr13:49075600-49093400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr13:49075600-49095200	Weak transcription	Fetal Intestine Large	intestine
19	chr13:49075800-49086000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr13:49075800-49088400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr13:49075800-49093200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr13:49076000-49084800	Weak transcription	Liver	Liver
23	chr13:49076000-49085800	Weak transcription	Fetal Kidney	kidney
24	chr13:49076600-49084800	Weak transcription	Brain Germinal Matrix	brain
25	chr13:49076600-49097400	Weak transcription	Pancreas	Pancrea
26	chr13:49077000-49085800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr13:49078000-49084400	Enhancers	Breast Myoepithelial Primary Cells	Breast
28	chr13:49078800-49084600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr13:49079600-49091000	Weak transcription	HUES6 Cell Line	embryonic stem cell
30	chr13:49079600-49092200	Weak transcription	HUES48 Cell Line	embryonic stem cell
31	chr13:49080400-49085800	Weak transcription	Psoas Muscle	Psoas
32	chr13:49080600-49085600	Weak transcription	Aorta	Aorta
33	chr13:49080600-49085800	Weak transcription	Rectal Mucosa Donor 29	rectum
34	chr13:49080600-49087800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr13:49080600-49105600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr13:49080800-49085800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
37	chr13:49080800-49086200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr13:49080800-49087400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr13:49080800-49102200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
40	chr13:49080800-49105400	Weak transcription	Duodenum Mucosa	Duodenum
41	chr13:49081000-49085600	Weak transcription	Brain Inferior Temporal Lobe	brain
42	chr13:49081000-49085800	Weak transcription	Muscle Satellite Cultured Cells	--
43	chr13:49081000-49085800	Weak transcription	HSMMtube	muscle
44	chr13:49081000-49090200	Weak transcription	HSMM	muscle
45	chr13:49081200-49084400	Weak transcription	Primary T cells from cord blood	blood
46	chr13:49081400-49084400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
47	chr13:49081400-49084400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
48	chr13:49081400-49084800	Weak transcription	Lung	lung
49	chr13:49081400-49085800	Weak transcription	Brain Angular Gyrus	brain
50	chr13:49081400-49085800	Weak transcription	Brain Hippocampus Middle	brain

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