Variant report

Variant	rs13185828
Chromosome Location	chr5:58430630-58430631
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 19 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs11955845	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13160617	0.81[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13164981	1.00[CEU][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs13174180	0.86[ASW][hapmap]
rs13178514	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13180599	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13185063	1.00[CEU][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs13185996	0.93[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs13186000	0.93[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs13186012	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];0.92[LWK][hapmap];0.96[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs13186015	0.93[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs16877155	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[GIH][hapmap];0.88[JPT][hapmap];0.92[LWK][hapmap];0.85[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs2059191	1.00[CEU][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2409627	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs33950471	0.87[CEU][hapmap];0.90[TSI][hapmap];0.81[EUR][1000 genomes]
rs34235034	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56273963	0.93[AFR][1000 genomes];0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs889229	0.81[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:1 , 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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs13185828	CCNO	cis	parietal	SCAN
rs13185828	LRRC70	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:58424000-58439800	Weak transcription	Small Intestine	intestine
2	chr5:58424000-58447000	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr5:58424200-58432800	Weak transcription	Right Ventricle	heart
4	chr5:58424200-58446200	Weak transcription	Fetal Intestine Large	intestine
5	chr5:58424200-58446600	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr5:58424400-58431400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
7	chr5:58426800-58431200	Enhancers	Primary T cells from cord blood	blood
8	chr5:58427200-58454000	Weak transcription	Primary neutrophils fromperipheralblood	blood
9	chr5:58428000-58431000	Enhancers	Skeletal Muscle Female	skeletal muscle
10	chr5:58428800-58435800	Weak transcription	Fetal Heart	heart
11	chr5:58429000-58430800	Enhancers	NHDF-Ad	bronchial
12	chr5:58429200-58431200	Enhancers	Hela-S3	cervix
13	chr5:58429400-58431200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr5:58429400-58431200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr5:58429600-58430800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr5:58429600-58430800	Enhancers	Osteobl	bone
17	chr5:58429600-58431000	Enhancers	HSMM	muscle
18	chr5:58429800-58431000	Enhancers	Fetal Lung	lung
19	chr5:58429800-58433800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr5:58429800-58447200	Weak transcription	Left Ventricle	heart
21	chr5:58430000-58430800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
22	chr5:58430000-58430800	Weak transcription	Aorta	Aorta
23	chr5:58430000-58432600	Weak transcription	Skeletal Muscle Male	skeletal muscle
24	chr5:58430000-58434400	Weak transcription	Psoas Muscle	Psoas
25	chr5:58430000-58437000	Weak transcription	Colon Smooth Muscle	Colon
26	chr5:58430000-58442600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr5:58430200-58430800	Enhancers	Pancreatic Islets	Pancreatic Islet
28	chr5:58430400-58432600	Weak transcription	Placenta Amnion	Placenta Amnion
29	chr5:58430600-58430800	Enhancers	Primary T helper cells fromperipheralblood	blood
30	chr5:58430600-58432600	Enhancers	A549	lung

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