Variant report

Variant	rs9568402
Chromosome Location	chr13:50961957-50961958
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:50891858..50893890-chr13:50960724..50962841,2	K562	blood:

Extended variants
information (count: 82 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs12428189	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12431131	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1327644	1.00[CEU][hapmap];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1359860	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs149846	0.81[ASN][1000 genomes]
rs17074346	0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17074358	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1924372	0.85[AFR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1924373	0.83[AFR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs201807	0.81[ASN][1000 genomes]
rs3116625	0.81[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs35824953	0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs471315	0.95[ASN][1000 genomes]
rs56023535	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56075206	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs58633776	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs60379059	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs61962133	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61962135	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs61964386	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs719103	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7327154	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7334326	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7983762	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7996632	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8000329	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8000875	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8000921	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9316495	0.83[CEU][hapmap];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9562962	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9562963	0.85[ASN][1000 genomes]
rs9562964	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9562965	0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9562966	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9562967	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9562968	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9562970	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9562972	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9562973	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9562974	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9562975	0.80[EUR][1000 genomes]
rs9562976	0.80[EUR][1000 genomes]
rs9562980	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9562981	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9562982	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9568397	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9568398	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9568399	0.84[ASN][1000 genomes]
rs9568400	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9568401	0.90[CEU][hapmap];0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9568403	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9568404	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9568405	0.91[ASN][1000 genomes]
rs9568406	1.00[CEU][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9568407	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9568408	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9568409	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9568410	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9568412	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9568413	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9568414	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9568415	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9568416	0.83[ASN][1000 genomes]
rs9568417	0.80[EUR][1000 genomes]
rs9568419	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9568422	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9568423	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9568424	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9568425	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9568427	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9568428	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9568429	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9568430	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9568431	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9634832	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9634833	0.80[AMR][1000 genomes]
rs9634834	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[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	nsv1035151	chr13:50513535-51167850	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1254 gene(s)	inside rSNPs	diseases
2	esv2753964	chr13:50545399-51421199	Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1256 gene(s)	inside rSNPs	diseases
3	esv2753492	chr13:50550081-51461720	Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1256 gene(s)	inside rSNPs	diseases
4	esv2752608	chr13:50550099-51054499	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1249 gene(s)	inside rSNPs	diseases
5	nsv832609	chr13:50946577-51065968	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:50950400-50967200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr13:50958600-50962800	Enhancers	Fetal Thymus	thymus
3	chr13:50959800-50962600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
4	chr13:50959800-50963000	Enhancers	H1 Cell Line	embryonic stem cell
5	chr13:50960000-50965000	Enhancers	HUES48 Cell Line	embryonic stem cell
6	chr13:50960400-50965000	Enhancers	iPS-15b Cell Line	embryonic stem cell
7	chr13:50960600-50965000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
8	chr13:50961200-50962000	Enhancers	Fetal Heart	heart
9	chr13:50961200-50962200	Active TSS	Skeletal Muscle Female	skeletal muscle
10	chr13:50961200-50964000	Weak transcription	HepG2	liver
11	chr13:50961200-50965400	Enhancers	HUVEC	blood vessel
12	chr13:50961400-50963000	Enhancers	H9 Cell Line	embryonic stem cell
13	chr13:50961400-50963000	Enhancers	Fetal Muscle Leg	muscle
14	chr13:50961400-50964800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr13:50961600-50962400	Enhancers	Fetal Muscle Trunk	muscle
16	chr13:50961600-50962400	Enhancers	HSMM	muscle
17	chr13:50961600-50962600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr13:50961600-50962600	Weak transcription	HUES6 Cell Line	embryonic stem cell
19	chr13:50961600-50962600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
20	chr13:50961600-50962600	Weak transcription	Sigmoid Colon	Sigmoid Colon
21	chr13:50961600-50963600	Weak transcription	Adipose Nuclei	Adipose
22	chr13:50961600-50963600	Weak transcription	Fetal Stomach	stomach
23	chr13:50961600-50964000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr13:50961600-50964000	Weak transcription	Lung	lung
25	chr13:50961600-50964200	Weak transcription	Duodenum Smooth Muscle	Duodenum
26	chr13:50961600-50964400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr13:50961600-50965000	Weak transcription	Pancreas	Pancrea
28	chr13:50961600-50966400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr13:50961600-50967600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
30	chr13:50961600-50967600	Weak transcription	Aorta	Aorta
31	chr13:50961600-50967800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr13:50961600-50967800	Weak transcription	Brain Hippocampus Middle	brain
33	chr13:50961600-50973800	Weak transcription	Brain Substantia Nigra	brain
34	chr13:50961600-50974200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr13:50961600-50974200	Weak transcription	Osteobl	bone
36	chr13:50961600-50974600	Weak transcription	Right Atrium	heart
37	chr13:50961800-50962000	Enhancers	Liver	Liver
38	chr13:50961800-50962000	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
39	chr13:50961800-50962200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr13:50961800-50962200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
41	chr13:50961800-50962600	Weak transcription	Fetal Kidney	kidney
42	chr13:50961800-50962600	Weak transcription	Thymus	Thymus
43	chr13:50961800-50962800	Weak transcription	HUES64 Cell Line	embryonic stem cell
44	chr13:50961800-50963600	Weak transcription	Left Ventricle	heart
45	chr13:50961800-50963600	Weak transcription	K562	blood
46	chr13:50961800-50963800	Weak transcription	Pancreatic Islets	Pancreatic Islet
47	chr13:50961800-50964000	Weak transcription	Fetal Lung	lung
48	chr13:50961800-50964800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr13:50961800-50967000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
50	chr13:50961800-50967000	Weak transcription	Cortex derived primary cultured neurospheres	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links