Variant report

Variant	rs253956
Chromosome Location	chr5:115666898-115666899
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 47 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10042163	0.90[CEU][hapmap];1.00[YRI][hapmap]
rs10044332	0.83[ASN][1000 genomes]
rs10055039	1.00[YRI][hapmap]
rs1090076	0.82[CEU][hapmap];1.00[JPT][hapmap]
rs11241386	0.86[ASN][1000 genomes]
rs12653124	0.83[CEU][hapmap]
rs12654057	0.81[ASN][1000 genomes]
rs1351136	0.83[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs1351137	0.83[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs1508874	0.90[CEU][hapmap];1.00[YRI][hapmap]
rs153591	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs153614	0.83[CEU][hapmap];0.89[CHB][hapmap];0.90[JPT][hapmap];0.83[YRI][hapmap]
rs168833	0.90[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.83[YRI][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17139652	0.80[ASN][1000 genomes]
rs187591	0.89[ASN][1000 genomes]
rs194182	0.91[CEU][hapmap];0.84[CHB][hapmap];0.85[JPT][hapmap]
rs1991446	0.83[ASN][1000 genomes]
rs2136206	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap]
rs253953	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs253960	0.91[CEU][hapmap];0.93[CHB][hapmap];0.89[JPT][hapmap];0.80[ASN][1000 genomes]
rs254149	0.84[CHB][hapmap]
rs254154	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs27499	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs27500	0.86[ASN][1000 genomes]
rs28125	0.91[CEU][hapmap];0.89[CHB][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs37182	0.91[CEU][hapmap];0.89[CHB][hapmap];0.90[JPT][hapmap]
rs3844070	0.83[ASN][1000 genomes]
rs4920906	1.00[YRI][hapmap]
rs6594955	0.83[YRI][hapmap]
rs6860795	0.91[CEU][hapmap];0.83[YRI][hapmap]
rs6878279	0.83[YRI][hapmap]
rs712580	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs712581	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72808983	0.87[ASN][1000 genomes]
rs784482	0.90[CEU][hapmap];0.89[CHB][hapmap];0.95[JPT][hapmap];0.82[YRI][hapmap];0.84[ASN][1000 genomes]
rs785368	0.83[CEU][hapmap]
rs804141	0.89[CEU][hapmap];0.90[JPT][hapmap]
rs804142	0.83[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs9285884	0.91[CEU][hapmap];0.83[YRI][hapmap]
rs9326992	0.90[CEU][hapmap];0.94[CHB][hapmap];0.81[JPT][hapmap];1.00[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv34146	chr5:115315944-115729919	Flanking Active TSS Enhancers ZNF genes & repeats Weak transcription Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
2	esv2755349	chr5:115384101-115733101	Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
3	nsv882746	chr5:115566026-115704566	Weak transcription Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv1017983	chr5:115578765-115713688	Weak transcription ZNF genes & repeats Active TSS Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv882748	chr5:115584159-115669950	ZNF genes & repeats Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv869754	chr5:115634234-115696094	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	nsv4968	chr5:115635771-115714856	Flanking Active TSS Strong transcription ZNF genes & repeats Weak transcription Bivalent/Poised TSS Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:115643200-115669800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr5:115644400-115671800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr5:115649000-115692800	Weak transcription	Fetal Heart	heart
4	chr5:115652000-115668000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr5:115653000-115667400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr5:115653600-115670400	Weak transcription	Right Ventricle	heart
7	chr5:115654600-115669600	Weak transcription	Duodenum Smooth Muscle	Duodenum
8	chr5:115655400-115669800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr5:115659200-115669600	Weak transcription	Fetal Kidney	kidney
10	chr5:115663200-115671000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr5:115663800-115667000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr5:115664600-115671600	Weak transcription	Stomach Smooth Muscle	stomach
13	chr5:115664800-115669600	Weak transcription	Rectal Mucosa Donor 31	rectum
14	chr5:115665200-115671800	Weak transcription	Ovary	ovary
15	chr5:115665400-115669400	Weak transcription	Skeletal Muscle Male	skeletal muscle
16	chr5:115665400-115669600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr5:115665400-115669600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr5:115665400-115669600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr5:115665400-115669600	Weak transcription	Aorta	Aorta
20	chr5:115665400-115669600	Weak transcription	Pancreas	Pancrea
21	chr5:115665400-115669600	Weak transcription	Thymus	Thymus
22	chr5:115665600-115669600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr5:115665600-115669600	Weak transcription	Esophagus	oesophagus
24	chr5:115665600-115669600	Weak transcription	Fetal Muscle Trunk	muscle
25	chr5:115665600-115669600	Weak transcription	Dnd41	blood
26	chr5:115665600-115670400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr5:115665800-115671000	Weak transcription	Primary T cells from cord blood	blood
28	chr5:115666400-115668800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr5:115666400-115669200	Weak transcription	Primary B cells from cord blood	blood
30	chr5:115666400-115669600	Weak transcription	Adipose Nuclei	Adipose
31	chr5:115666400-115669800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr5:115666400-115670000	Weak transcription	Rectal Mucosa Donor 29	rectum
33	chr5:115666600-115669600	Weak transcription	Liver	Liver
34	chr5:115666600-115669800	Weak transcription	Cortex derived primary cultured neurospheres	brain
35	chr5:115666800-115668800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
36	chr5:115666800-115669200	Weak transcription	Monocytes-CD14+_RO01746	blood
37	chr5:115666800-115669800	Weak transcription	Fetal Lung	lung
38	chr5:115666800-115683600	Weak transcription	Skeletal Muscle Female	skeletal muscle

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