Variant report

Variant	rs1971940
Chromosome Location	chr5:58460599-58460600
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 16 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs13176291	0.81[CEU][hapmap];0.86[MEX][hapmap]
rs13176475	0.81[CEU][hapmap];0.86[MEX][hapmap]
rs13361218	0.90[CEU][hapmap];0.90[MEX][hapmap]
rs1559251	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]
rs1824788	0.83[CHD][hapmap]
rs28385324	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.88[ASN][1000 genomes]
rs4699935	0.86[ASN][1000 genomes]
rs4700322	0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6450506	0.90[CEU][hapmap];0.86[CHB][hapmap];0.89[CHD][hapmap];0.91[JPT][hapmap];0.91[MEX][hapmap];0.82[ASN][1000 genomes]
rs716908	0.90[CEU][hapmap];0.86[CHB][hapmap];0.84[CHD][hapmap];0.91[JPT][hapmap];0.80[ASN][1000 genomes]
rs7707065	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7728050	1.00[ASW][hapmap];1.00[CEU][hapmap];0.81[CHD][hapmap];0.93[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7730750	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs922434	0.90[CEU][hapmap]

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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1971940	CCNO	cis	parietal	SCAN
rs1971940	LRRC70	cis	cerebellum	SCAN
rs1971940	IPO11	cis	cerebellum	SCAN

Chromatin state (count:34 , 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	chr5:58449400-58473600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
8	chr5:58449800-58489400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr5:58452200-58464000	Weak transcription	Hela-S3	cervix
10	chr5:58454200-58465000	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr5:58454400-58472800	Weak transcription	Stomach Smooth Muscle	stomach
12	chr5:58455200-58473400	Weak transcription	Fetal Muscle Leg	muscle
13	chr5:58455800-58473600	Weak transcription	Primary neutrophils fromperipheralblood	blood
14	chr5:58456000-58460600	Weak transcription	Colon Smooth Muscle	Colon
15	chr5:58456600-58464000	Weak transcription	Psoas Muscle	Psoas
16	chr5:58457800-58473400	Weak transcription	Fetal Intestine Small	intestine
17	chr5:58458000-58463600	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr5:58458600-58462200	Weak transcription	Thymus	Thymus
19	chr5:58459000-58460600	Weak transcription	Fetal Thymus	thymus
20	chr5:58459200-58460800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr5:58459400-58460800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr5:58459400-58460800	Enhancers	Muscle Satellite Cultured Cells	--
23	chr5:58459400-58473400	Weak transcription	Fetal Stomach	stomach
24	chr5:58459600-58460600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr5:58459600-58460800	Enhancers	Pancreatic Islets	Pancreatic Islet
26	chr5:58459600-58460800	Enhancers	Fetal Lung	lung
27	chr5:58459600-58460800	Enhancers	NHDF-Ad	bronchial
28	chr5:58459800-58460800	Enhancers	NHLF	lung
29	chr5:58460000-58460600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr5:58460000-58472600	Weak transcription	Rectal Mucosa Donor 29	rectum
31	chr5:58460200-58460800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr5:58460200-58460800	Flanking Active TSS	A549	lung
33	chr5:58460400-58460800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr5:58460400-58460800	Enhancers	Osteobl	bone

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