Variant report

Variant	rs1559251
Chromosome Location	chr5:58455403-58455404
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 22 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10062340	0.82[CHB][hapmap];0.82[CHD][hapmap]
rs10062397	0.81[CHB][hapmap]
rs1038080	0.86[CHB][hapmap]
rs10472093	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13176291	0.90[CEU][hapmap];0.91[GIH][hapmap];0.95[MEX][hapmap];0.87[TSI][hapmap]
rs13176475	0.90[CEU][hapmap];0.87[GIH][hapmap];0.95[MEX][hapmap];0.90[TSI][hapmap]
rs13361218	1.00[CEU][hapmap];0.81[CHD][hapmap];0.91[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1551939	0.85[CHB][hapmap]
rs1971940	0.90[CEU][hapmap];0.91[CHB][hapmap];0.89[CHD][hapmap];0.86[JPT][hapmap];0.91[MEX][hapmap];0.83[ASN][1000 genomes]
rs28385324	0.82[CEU][hapmap];0.91[CHB][hapmap];0.89[CHD][hapmap];0.82[JPT][hapmap];0.95[MEX][hapmap]
rs6450506	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6875867	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs716908	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.82[LWK][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7707065	0.82[ASN][1000 genomes]
rs7707392	0.81[CHB][hapmap]
rs7707566	0.82[CHB][hapmap]
rs7728050	0.90[CEU][hapmap];0.91[MEX][hapmap]
rs7730750	0.82[ASN][1000 genomes]
rs922434	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9292193	0.88[EUR][1000 genomes];0.92[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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1559251	LRRC70	cis	cerebellum	SCAN
rs1559251	CCNO	cis	parietal	SCAN

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:58439000-58484000	Weak transcription	Fetal Kidney	kidney
2	chr5:58447600-58464000	Weak transcription	Right Ventricle	heart
3	chr5:58447600-58465200	Weak transcription	Right Atrium	heart
4	chr5:58447600-58473200	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr5:58447600-58473400	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr5:58447600-58479600	Weak transcription	Left Ventricle	heart
7	chr5:58449000-58456400	Weak transcription	Fetal Intestine Large	intestine
8	chr5:58449200-58457000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
9	chr5:58449200-58457600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
10	chr5:58449400-58473600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
11	chr5:58449600-58457000	Weak transcription	Primary T helper cells fromperipheralblood	blood
12	chr5:58449800-58456400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
13	chr5:58449800-58489400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr5:58450000-58460200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr5:58451400-58459600	Weak transcription	Fetal Lung	lung
16	chr5:58452000-58456800	Weak transcription	Fetal Thymus	thymus
17	chr5:58452000-58457000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
18	chr5:58452200-58464000	Weak transcription	Hela-S3	cervix
19	chr5:58452800-58458200	Genic enhancers	A549	lung
20	chr5:58453000-58455800	Enhancers	Fetal Heart	heart
21	chr5:58453000-58456000	Enhancers	Colon Smooth Muscle	Colon
22	chr5:58453400-58457000	Weak transcription	Primary T cells from cord blood	blood
23	chr5:58453800-58456000	Enhancers	Pancreatic Islets	Pancreatic Islet
24	chr5:58453800-58456000	Enhancers	Psoas Muscle	Psoas
25	chr5:58454000-58455800	Enhancers	Primary neutrophils fromperipheralblood	blood
26	chr5:58454000-58455800	Enhancers	Rectal Smooth Muscle	rectum
27	chr5:58454000-58455800	Enhancers	Skeletal Muscle Female	skeletal muscle
28	chr5:58454000-58459400	Weak transcription	Muscle Satellite Cultured Cells	--
29	chr5:58454200-58465000	Weak transcription	Skeletal Muscle Male	skeletal muscle
30	chr5:58454400-58455800	Weak transcription	Duodenum Smooth Muscle	Duodenum
31	chr5:58454400-58472800	Weak transcription	Stomach Smooth Muscle	stomach
32	chr5:58454800-58457000	Weak transcription	Placenta Amnion	Placenta Amnion
33	chr5:58454800-58459800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr5:58454800-58459800	Weak transcription	HSMM	muscle
35	chr5:58455200-58473400	Weak transcription	Fetal Muscle Leg	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links