Variant report

Variant	rs56153113
Chromosome Location	chr5:98359700-98359701
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 86 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:83)

rs_ID	r²[population]
rs10039507	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10040675	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10041263	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10041335	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10054523	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10055595	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10056842	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10056918	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10061406	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10062455	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10064594	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10065808	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10067635	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10067866	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10068003	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10068917	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10077697	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10085106	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10085145	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10479350	0.98[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10479351	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10479352	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10479353	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10479354	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11948998	0.83[EUR][1000 genomes]
rs11952820	0.81[EUR][1000 genomes]
rs11953096	0.83[EUR][1000 genomes]
rs11958835	0.83[EUR][1000 genomes]
rs12332280	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12332340	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12332364	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12332383	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs161742	0.98[EUR][1000 genomes]
rs17166414	0.89[EUR][1000 genomes]
rs17166423	0.89[EUR][1000 genomes]
rs17166428	0.83[EUR][1000 genomes]
rs17166439	0.89[EUR][1000 genomes]
rs17166455	0.91[EUR][1000 genomes]
rs17166484	0.95[EUR][1000 genomes]
rs17166575	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17166578	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2164986	0.89[EUR][1000 genomes]
rs28555343	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs28656032	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2963709	0.95[EUR][1000 genomes]
rs327810	0.85[EUR][1000 genomes]
rs36011435	0.89[EUR][1000 genomes]
rs44070	0.98[EUR][1000 genomes]
rs55780476	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55821667	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55854720	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs56046686	0.89[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs56086412	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56096102	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs56115002	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56159022	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs56160758	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56246849	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs56311403	0.91[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs56331326	0.85[EUR][1000 genomes]
rs56331947	0.95[EUR][1000 genomes]
rs56400831	0.89[EUR][1000 genomes]
rs58479016	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58771325	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6596659	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6866629	0.81[EUR][1000 genomes]
rs6867271	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6880359	0.83[EUR][1000 genomes]
rs6883467	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6885458	0.80[AFR][1000 genomes]
rs6890358	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6895358	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs727637	0.83[EUR][1000 genomes]
rs73776017	0.83[EUR][1000 genomes]
rs73776027	0.83[EUR][1000 genomes]
rs73776028	0.83[EUR][1000 genomes]
rs7708436	0.95[EUR][1000 genomes]
rs7719375	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7726329	0.83[EUR][1000 genomes]
rs7737402	0.98[EUR][1000 genomes]
rs9327950	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9327954	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9327955	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1024391	chr5:98355665-98653657	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
2	nsv599118	chr5:98358191-99029453	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	nsv599119	chr5:98358191-99315677	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:98353600-98361600	Weak transcription	Small Intestine	intestine
2	chr5:98356000-98360600	Weak transcription	Colonic Mucosa	Colon
3	chr5:98356400-98360400	Weak transcription	Duodenum Smooth Muscle	Duodenum
4	chr5:98356400-98360400	Weak transcription	GM12878-XiMat	blood
5	chr5:98356400-98361000	Weak transcription	Primary hematopoietic stem cells	blood
6	chr5:98356400-98361000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr5:98356400-98361000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr5:98356400-98361200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
9	chr5:98356400-98361200	Weak transcription	Fetal Stomach	stomach
10	chr5:98356400-98361600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
11	chr5:98356400-98361800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr5:98356400-98362400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr5:98356800-98361000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr5:98356800-98361000	Weak transcription	A549	lung
15	chr5:98356800-98361000	Weak transcription	HUVEC	blood vessel
16	chr5:98356800-98361200	Weak transcription	Adipose Nuclei	Adipose
17	chr5:98357000-98360200	Weak transcription	Liver	Liver
18	chr5:98357000-98360400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr5:98357000-98361200	Enhancers	Monocytes-CD14+_RO01746	blood
20	chr5:98357000-98362000	Weak transcription	Cortex derived primary cultured neurospheres	brain
21	chr5:98357200-98360200	Weak transcription	Rectal Mucosa Donor 29	rectum
22	chr5:98357400-98360200	Weak transcription	Duodenum Mucosa	Duodenum
23	chr5:98357400-98368400	Enhancers	Primary monocytes fromperipheralblood	blood
24	chr5:98358200-98360000	Weak transcription	Rectal Mucosa Donor 31	rectum
25	chr5:98358200-98366800	Weak transcription	K562	blood
26	chr5:98358400-98360000	Weak transcription	Sigmoid Colon	Sigmoid Colon
27	chr5:98358400-98360000	Weak transcription	HepG2	liver
28	chr5:98358400-98360200	Weak transcription	Fetal Intestine Small	intestine
29	chr5:98358600-98360000	Weak transcription	Fetal Intestine Large	intestine
30	chr5:98358800-98360000	Weak transcription	Stomach Mucosa	stomach

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links