Variant report

Variant	rs295956
Chromosome Location	chr5:58901374-58901375
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 91 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:85)

rs_ID	r²[population]
rs10805516	1.00[CEU][hapmap];0.89[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs159194	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs159196	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.93[ASN][1000 genomes]
rs159197	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs177077	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs177078	0.89[ASN][1000 genomes]
rs186078	0.88[ASN][1000 genomes]
rs190936	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs294477	0.88[ASN][1000 genomes]
rs294478	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs294479	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs294481	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs294482	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs294483	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs294484	0.83[CEU][hapmap];1.00[CHB][hapmap];0.83[YRI][hapmap];0.89[ASN][1000 genomes]
rs294485	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs294486	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs294492	1.00[ASW][hapmap];0.86[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.89[MEX][hapmap];0.95[YRI][hapmap];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs294494	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs294495	0.96[ASN][1000 genomes]
rs294496	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.96[ASN][1000 genomes]
rs294497	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs294498	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs294499	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs294500	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs294501	0.93[ASN][1000 genomes]
rs294502	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs295943	0.86[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.86[TSI][hapmap];0.93[EUR][1000 genomes]
rs295944	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.89[AFR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs295946	0.92[CHB][hapmap];0.90[JPT][hapmap]
rs295948	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs295950	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs295951	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs295952	0.92[CHB][hapmap];0.82[JPT][hapmap]
rs295953	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs295954	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs295955	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs295957	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs295958	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs295960	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs295962	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs295963	1.00[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.89[MEX][hapmap];1.00[MKK][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs295964	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs295965	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs295966	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs295967	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs295968	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs295969	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs295970	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs295971	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs295972	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs295973	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs295974	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs295975	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs295978	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs295979	0.93[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs295980	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs298014	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.93[TSI][hapmap];0.89[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs298016	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs298017	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs298025	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs298027	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs298028	1.00[CHB][hapmap];0.82[CHD][hapmap];0.90[JPT][hapmap]
rs298029	1.00[CHB][hapmap];0.82[CHD][hapmap];0.90[JPT][hapmap]
rs298030	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs298032	1.00[CHB][hapmap];0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs298033	0.92[CHB][hapmap];0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs298034	0.87[ASW][hapmap];0.92[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs298036	0.89[ASN][1000 genomes]
rs298038	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs298039	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs298040	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs298041	0.89[ASN][1000 genomes]
rs298043	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs298044	0.87[ASW][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs298045	0.87[ASW][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs298046	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs298047	0.89[ASN][1000 genomes]
rs298048	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs298051	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs298052	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.93[TSI][hapmap];0.89[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs298053	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs37569	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs37570	0.89[ASN][1000 genomes]
rs37571	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv598254	chr5:58715782-58923601	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
2	nsv1031631	chr5:58783629-59015470	Enhancers Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA	4 gene(s)	inside rSNPs	diseases
3	nsv881708	chr5:58869051-59093198	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA	11 gene(s)	inside rSNPs	diseases
4	nsv1018015	chr5:58889470-59532667	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
5	nsv537766	chr5:58889470-59532667	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
6	nsv598256	chr5:58893286-58939840	Active TSS Enhancers Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:58884200-58902800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr5:58894600-58901400	Weak transcription	HUES6 Cell Line	embryonic stem cell
3	chr5:58894600-58902000	Weak transcription	Brain Germinal Matrix	brain
4	chr5:58894800-58902400	Weak transcription	Fetal Lung	lung
5	chr5:58894800-58902800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr5:58894800-58903000	Weak transcription	Psoas Muscle	Psoas
7	chr5:58894800-58903400	Weak transcription	Fetal Kidney	kidney
8	chr5:58894800-58904800	Weak transcription	HSMMtube	muscle
9	chr5:58894800-58910800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr5:58894800-58910800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr5:58895800-58911200	Weak transcription	Hela-S3	cervix
12	chr5:58896200-58902800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr5:58897000-58903000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr5:58897200-58902600	Weak transcription	Brain Anterior Caudate	brain
15	chr5:58897200-58903000	Weak transcription	Brain Angular Gyrus	brain
16	chr5:58897400-58902400	Weak transcription	Colon Smooth Muscle	Colon
17	chr5:58897600-58902000	Weak transcription	Pancreatic Islets	Pancreatic Islet
18	chr5:58897600-58905800	Weak transcription	Stomach Mucosa	stomach
19	chr5:58897600-58915800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr5:58900600-58902800	Weak transcription	Skeletal Muscle Female	skeletal muscle
21	chr5:58901000-58902400	Weak transcription	A549	lung
22	chr5:58901200-58904400	Enhancers	Fetal Brain Male	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links