Variant report

Variant	rs11960474
Chromosome Location	chr5:97762090-97762091
allele	A/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:34)

rs_ID	r²[population]
rs10043610	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10067255	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10478264	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10515275	0.88[CEU][hapmap];0.86[CHB][hapmap];0.85[JPT][hapmap];0.85[EUR][1000 genomes]
rs11241318	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11744068	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13161187	0.84[CEU][hapmap];0.90[CHB][hapmap];0.83[JPT][hapmap];0.83[EUR][1000 genomes]
rs13185967	0.88[CEU][hapmap];0.86[CHB][hapmap];0.85[JPT][hapmap];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13190416	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1378439	0.96[CEU][hapmap];0.96[CHB][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1378440	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1378441	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1455418	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1455419	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1455420	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1455422	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1455423	0.85[CEU][hapmap];0.91[CHB][hapmap];0.86[JPT][hapmap];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17165927	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2219186	0.85[EUR][1000 genomes]
rs2887280	0.96[CEU][hapmap];0.96[CHB][hapmap];0.95[JPT][hapmap];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34750082	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35371994	0.85[EUR][1000 genomes]
rs4703069	0.85[CEU][hapmap];0.91[CHB][hapmap];0.86[JPT][hapmap];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs56218605	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56308227	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs61434460	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6594728	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6859633	0.89[CEU][hapmap];0.91[CHB][hapmap];0.86[JPT][hapmap];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7713002	0.89[CEU][hapmap];0.96[CHB][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7719654	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7727877	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9326967	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9326968	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs961713	0.88[CEU][hapmap];0.86[CHB][hapmap];0.85[JPT][hapmap];0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv882407	chr5:97553255-97783046	Active TSS Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv882408	chr5:97616089-97836794	Enhancers Strong transcription ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv830419	chr5:97653713-97829079	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
4	nsv1018555	chr5:97719032-97873906	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
5	nsv882409	chr5:97761687-97817930	Enhancers Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	n/a	n/a	inside rSNPs	diseases

No data

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:97755200-97763800	Weak transcription	Small Intestine	intestine
2	chr5:97755200-97764400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr5:97760200-97762600	Enhancers	Fetal Stomach	stomach
4	chr5:97760400-97762400	Enhancers	Colon Smooth Muscle	Colon
5	chr5:97760800-97763000	Enhancers	Duodenum Smooth Muscle	Duodenum
6	chr5:97761200-97762600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr5:97761200-97764400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr5:97761200-97764400	Enhancers	NHDF-Ad	bronchial
9	chr5:97761400-97767800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr5:97761600-97762600	Enhancers	Stomach Smooth Muscle	stomach
11	chr5:97761600-97763200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr5:97761600-97763400	Weak transcription	HSMM	muscle
13	chr5:97761600-97764400	Weak transcription	Osteobl	bone
14	chr5:97761800-97762400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
15	chr5:97761800-97763800	Weak transcription	Muscle Satellite Cultured Cells	--
16	chr5:97761800-97764800	Weak transcription	HSMMtube	muscle
17	chr5:97762000-97762200	Enhancers	HUES48 Cell Line	embryonic stem cell
18	chr5:97762000-97762600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr5:97762000-97762800	Weak transcription	Fetal Muscle Leg	muscle
20	chr5:97762000-97763400	Weak transcription	NHLF	lung
21	chr5:97762000-97764800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin

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