Variant report

Variant	rs6896497
Chromosome Location	chr5:58453662-58453663
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 39 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10036938	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10042606	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10064744	0.89[CEU][hapmap];0.81[EUR][1000 genomes]
rs10077198	0.86[ASN][1000 genomes]
rs10472094	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10472095	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1077978	0.89[CEU][hapmap]
rs11948460	0.86[ASN][1000 genomes]
rs12108992	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12516263	0.93[ASN][1000 genomes]
rs13357070	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16889248	0.83[CEU][hapmap];0.80[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs16889254	0.89[CEU][hapmap];0.80[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs16889258	0.89[CEU][hapmap];0.80[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs28540859	1.00[ASN][1000 genomes]
rs28705844	0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62356728	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs62357974	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6450504	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6450505	0.81[CEU][hapmap];1.00[CHB][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6450508	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6450509	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6868963	0.88[CEU][hapmap];1.00[CHB][hapmap];0.80[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs6869149	0.89[CEU][hapmap];0.80[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs6874089	0.94[CEU][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6881137	0.82[EUR][1000 genomes]
rs6883912	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6886854	0.82[EUR][1000 genomes]
rs6892369	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7700594	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7714707	0.88[CEU][hapmap];0.93[ASN][1000 genomes]
rs7728221	0.94[CEU][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7735375	0.80[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs8180396	0.89[CEU][hapmap]
rs922436	0.96[ASN][1000 genomes]
rs9292191	0.83[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs9918111	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2830363	chr5:57893949-58555491	Weak transcription Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
2	nsv881702	chr5:58432413-58474854	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:58427200-58454000	Weak transcription	Primary neutrophils fromperipheralblood	blood
2	chr5:58437400-58454000	Weak transcription	Rectal Smooth Muscle	rectum
3	chr5:58439000-58484000	Weak transcription	Fetal Kidney	kidney
4	chr5:58447600-58454800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr5:58447600-58464000	Weak transcription	Right Ventricle	heart
6	chr5:58447600-58465200	Weak transcription	Right Atrium	heart
7	chr5:58447600-58473200	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr5:58447600-58473400	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr5:58447600-58479600	Weak transcription	Left Ventricle	heart
10	chr5:58449000-58453800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
11	chr5:58449000-58453800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr5:58449000-58456400	Weak transcription	Fetal Intestine Large	intestine
13	chr5:58449200-58453800	Weak transcription	Pancreatic Islets	Pancreatic Islet
14	chr5:58449200-58454200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr5:58449200-58457000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
16	chr5:58449200-58457600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
17	chr5:58449400-58473600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
18	chr5:58449600-58453800	Weak transcription	Psoas Muscle	Psoas
19	chr5:58449600-58457000	Weak transcription	Primary T helper cells fromperipheralblood	blood
20	chr5:58449800-58453800	Weak transcription	Small Intestine	intestine
21	chr5:58449800-58454000	Weak transcription	Skeletal Muscle Female	skeletal muscle
22	chr5:58449800-58456400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
23	chr5:58449800-58489400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr5:58450000-58460200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr5:58451400-58459600	Weak transcription	Fetal Lung	lung
26	chr5:58451600-58455200	Enhancers	Fetal Muscle Leg	muscle
27	chr5:58452000-58456800	Weak transcription	Fetal Thymus	thymus
28	chr5:58452000-58457000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
29	chr5:58452200-58454800	Enhancers	HSMM	muscle
30	chr5:58452200-58455000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
31	chr5:58452200-58464000	Weak transcription	Hela-S3	cervix
32	chr5:58452800-58454000	Enhancers	Muscle Satellite Cultured Cells	--
33	chr5:58452800-58454200	Enhancers	HSMMtube	muscle
34	chr5:58452800-58458200	Genic enhancers	A549	lung
35	chr5:58453000-58455800	Enhancers	Fetal Heart	heart
36	chr5:58453000-58456000	Enhancers	Colon Smooth Muscle	Colon
37	chr5:58453400-58454000	Enhancers	iPS-18 Cell Line	embryonic stem cell
38	chr5:58453400-58454200	Enhancers	Skeletal Muscle Male	skeletal muscle
39	chr5:58453400-58454800	Enhancers	Placenta Amnion	Placenta Amnion
40	chr5:58453400-58457000	Weak transcription	Primary T cells from cord blood	blood
41	chr5:58453600-58453800	Enhancers	HUES64 Cell Line	embryonic stem cell
42	chr5:58453600-58454400	Enhancers	Duodenum Smooth Muscle	Duodenum

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