Variant report

Variant	rs6450505
Chromosome Location	chr5:58458252-58458253
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	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10042606	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10064744	0.83[CEU][hapmap]
rs10077198	0.86[ASN][1000 genomes]
rs10472094	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10472095	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1077978	0.84[CEU][hapmap]
rs11948460	0.86[ASN][1000 genomes]
rs12108992	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12516263	0.93[ASN][1000 genomes]
rs13357070	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16889248	0.80[ASN][1000 genomes]
rs16889254	0.89[ASN][1000 genomes]
rs16889258	0.93[ASN][1000 genomes]
rs28540859	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28705844	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62356728	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62357974	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6450504	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6450508	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6450509	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6868963	1.00[CHB][hapmap];0.86[ASN][1000 genomes]
rs6869149	0.83[CEU][hapmap];0.93[ASN][1000 genomes]
rs6874089	0.89[CEU][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6881137	0.81[EUR][1000 genomes]
rs6883912	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6886854	0.81[EUR][1000 genomes]
rs6892369	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6896497	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]
rs7700594	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7714707	0.81[CEU][hapmap];0.93[ASN][1000 genomes]
rs7728221	0.89[CEU][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7735375	0.93[ASN][1000 genomes]
rs8180396	0.80[CEU][hapmap]
rs922436	0.96[ASN][1000 genomes]
rs9292191	0.80[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs9918111	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[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:30 , 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	chr5:58450000-58460200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr5:58451400-58459600	Weak transcription	Fetal Lung	lung
11	chr5:58452200-58464000	Weak transcription	Hela-S3	cervix
12	chr5:58454000-58459400	Weak transcription	Muscle Satellite Cultured Cells	--
13	chr5:58454200-58465000	Weak transcription	Skeletal Muscle Male	skeletal muscle
14	chr5:58454400-58472800	Weak transcription	Stomach Smooth Muscle	stomach
15	chr5:58454800-58459800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr5:58454800-58459800	Weak transcription	HSMM	muscle
17	chr5:58455200-58473400	Weak transcription	Fetal Muscle Leg	muscle
18	chr5:58455800-58473600	Weak transcription	Primary neutrophils fromperipheralblood	blood
19	chr5:58456000-58459600	Weak transcription	Pancreatic Islets	Pancreatic Islet
20	chr5:58456000-58460600	Weak transcription	Colon Smooth Muscle	Colon
21	chr5:58456400-58458400	Enhancers	Fetal Intestine Large	intestine
22	chr5:58456600-58464000	Weak transcription	Psoas Muscle	Psoas
23	chr5:58456800-58459000	Enhancers	Fetal Thymus	thymus
24	chr5:58457000-58458400	Enhancers	Primary T helper cells fromperipheralblood	blood
25	chr5:58457000-58458600	Enhancers	Primary T cells from cord blood	blood
26	chr5:58457200-58458400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
27	chr5:58457200-58458600	Enhancers	Thymus	Thymus
28	chr5:58457800-58473400	Weak transcription	Fetal Intestine Small	intestine
29	chr5:58458000-58463600	Weak transcription	Placenta Amnion	Placenta Amnion
30	chr5:58458200-58459600	Weak transcription	A549	lung

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