Variant report

Variant	rs966329
Chromosome Location	chr6:55690339-55690340
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10485076	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs1073472	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs10807505	0.94[EUR][1000 genomes]
rs10948955	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1374551	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1447129	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs1470527	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs16887283	0.91[EUR][1000 genomes]
rs1947135	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1947136	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2023522	0.94[EUR][1000 genomes]
rs2023523	0.94[EUR][1000 genomes]
rs3798830	0.94[EUR][1000 genomes]
rs3798836	0.85[CHB][hapmap];0.90[JPT][hapmap];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3823038	0.88[CEU][hapmap];0.89[EUR][1000 genomes]
rs56191021	0.91[EUR][1000 genomes]
rs6459108	1.00[CEU][hapmap];0.81[YRI][hapmap];0.94[EUR][1000 genomes]
rs6914731	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6929620	0.85[CEU][hapmap];0.86[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7749016	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs7749809	0.96[CEU][hapmap];0.91[EUR][1000 genomes]
rs7750450	0.96[CEU][hapmap];0.90[EUR][1000 genomes]
rs7752801	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs7767441	0.96[CEU][hapmap];0.91[EUR][1000 genomes]
rs9296803	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9367665	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9367667	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs9475428	0.96[CEU][hapmap];0.92[YRI][hapmap];0.82[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs9475429	0.96[CEU][hapmap];0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1034037	chr6:55222409-56069600	Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	esv2752670	chr6:55614978-55781605	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
3	nsv1032684	chr6:55680473-55766876	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:55684000-55692000	Weak transcription	Fetal Brain Male	brain
2	chr6:55687200-55692400	Weak transcription	HepG2	liver
3	chr6:55687400-55690600	Enhancers	HSMMtube	muscle
4	chr6:55687800-55690600	Enhancers	Breast Myoepithelial Primary Cells	Breast
5	chr6:55687800-55693200	Enhancers	Pancreatic Islets	Pancreatic Islet
6	chr6:55687800-55693200	Enhancers	HMEC	breast
7	chr6:55687800-55693800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr6:55688000-55690400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr6:55688200-55693400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr6:55688600-55690600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr6:55688800-55692000	Enhancers	Fetal Intestine Small	intestine
12	chr6:55689000-55690800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr6:55689000-55691000	Enhancers	Fetal Lung	lung
14	chr6:55689200-55690800	Enhancers	Colon Smooth Muscle	Colon
15	chr6:55689200-55691200	Enhancers	A549	lung
16	chr6:55689200-55693200	Enhancers	NHEK	skin
17	chr6:55689200-55693400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr6:55689400-55690400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr6:55689400-55690800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr6:55689400-55690800	Enhancers	Fetal Kidney	kidney
21	chr6:55689600-55690400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr6:55689600-55690600	Enhancers	HSMM	muscle
23	chr6:55689600-55691000	Enhancers	NHDF-Ad	bronchial
24	chr6:55689800-55690400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr6:55690000-55690600	Enhancers	Muscle Satellite Cultured Cells	--
26	chr6:55690000-55691000	Flanking Active TSS	Fetal Heart	heart
27	chr6:55690200-55690800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr6:55690200-55690800	Enhancers	Duodenum Smooth Muscle	Duodenum
29	chr6:55690200-55690800	Enhancers	Osteobl	bone
30	chr6:55690200-55691000	Enhancers	NH-A	brain
31	chr6:55690200-55691000	Enhancers	NHLF	lung
32	chr6:55690200-55691200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr6:55690200-55691400	Weak transcription	Fetal Intestine Large	intestine

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