Variant report

Variant	rs3799606
Chromosome Location	chr6:166993078-166993079
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 15 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs3778390	0.85[ASN][1000 genomes]
rs3778391	0.85[ASN][1000 genomes]
rs3799607	0.83[ASN][1000 genomes]
rs4710069	0.87[CHB][hapmap];0.82[JPT][hapmap];0.93[ASN][1000 genomes]
rs4710070	0.87[CHB][hapmap];0.83[ASN][1000 genomes]
rs56064314	0.84[ASN][1000 genomes]
rs9295353	0.87[CHB][hapmap];0.85[ASN][1000 genomes]
rs9355584	0.82[CEU][hapmap]
rs9457189	0.96[CEU][hapmap];0.87[CHB][hapmap];0.91[JPT][hapmap];0.93[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3490076	chr6:166727901-167306743	Strong transcription Weak transcription Flanking Active TSS Genic enhancers Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	25 gene(s)	inside rSNPs	diseases
2	esv3490077	chr6:166727901-167306743	Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	25 gene(s)	inside rSNPs	diseases
3	nsv886941	chr6:166907173-166996991	Strong transcription Weak transcription Genic enhancers Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA	5 gene(s)	inside rSNPs	diseases
4	nsv5592	chr6:166958317-167002951	Weak transcription Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv1029530	chr6:166977678-167016052	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv605260	chr6:166984094-167455139	Enhancers Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:166979400-166996600	Weak transcription	Primary neutrophils fromperipheralblood	blood
2	chr6:166979400-166997600	Weak transcription	Stomach Smooth Muscle	stomach
3	chr6:166981800-167002400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr6:166986000-166996400	Weak transcription	Fetal Kidney	kidney
5	chr6:166986200-167002200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr6:166986600-166994800	Weak transcription	Pancreas	Pancrea
7	chr6:166986600-167001400	Weak transcription	Brain Hippocampus Middle	brain
8	chr6:166986800-166994800	Weak transcription	Gastric	stomach
9	chr6:166986800-166997800	Weak transcription	Brain Substantia Nigra	brain
10	chr6:166986800-167003000	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr6:166987000-166993600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr6:166987000-166994800	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr6:166987000-166995400	Weak transcription	Spleen	Spleen
14	chr6:166987000-166996600	Weak transcription	Osteobl	bone
15	chr6:166987000-166997200	Weak transcription	Brain Cingulate Gyrus	brain
16	chr6:166987000-167002000	Weak transcription	Duodenum Mucosa	Duodenum
17	chr6:166987200-166995000	Weak transcription	Brain Angular Gyrus	brain
18	chr6:166987200-166997600	Weak transcription	NHLF	lung
19	chr6:166987200-166998400	Weak transcription	NH-A	brain
20	chr6:166987200-167001800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr6:166987800-166994800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr6:166987800-166996600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr6:166989000-166996600	Weak transcription	Esophagus	oesophagus
24	chr6:166989000-167011400	Weak transcription	Ovary	ovary
25	chr6:166989600-167001800	Weak transcription	Skeletal Muscle Male	skeletal muscle
26	chr6:166990000-166993200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr6:166990600-167001800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr6:166991600-166997800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr6:166991600-166998800	Enhancers	Fetal Brain Male	brain
30	chr6:166991800-166993400	Enhancers	Brain Germinal Matrix	brain
31	chr6:166991800-166993800	Enhancers	Fetal Brain Female	brain
32	chr6:166991800-166996000	Enhancers	Fetal Muscle Trunk	muscle
33	chr6:166991800-166996600	Weak transcription	H1 Cell Line	embryonic stem cell
34	chr6:166992000-166993800	Enhancers	Fetal Stomach	stomach
35	chr6:166992000-166995600	Weak transcription	Muscle Satellite Cultured Cells	--
36	chr6:166992000-166998800	Enhancers	Fetal Muscle Leg	muscle
37	chr6:166992200-166993600	Enhancers	HSMMtube	muscle
38	chr6:166992400-166993400	Weak transcription	Right Ventricle	heart
39	chr6:166992400-166993600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr6:166992400-166993800	Weak transcription	Skeletal Muscle Female	skeletal muscle
41	chr6:166992400-166994200	Enhancers	Left Ventricle	heart
42	chr6:166992400-166995400	Weak transcription	Lung	lung
43	chr6:166992400-167000200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr6:166992400-167000400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr6:166992600-166993600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr6:166992600-166993800	Enhancers	Fetal Heart	heart
47	chr6:166992800-166993400	Enhancers	Cortex derived primary cultured neurospheres	brain
48	chr6:166992800-166993600	Enhancers	HSMM	muscle
49	chr6:166993000-166993600	Enhancers	ES-I3 Cell Line	embryonic stem cell
50	chr6:166993000-166993600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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