Variant report

Variant	rs3778379
Chromosome Location	chr6:167007297-167007298
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:167005324..167007495-chr6:167014503..167017118,2	MCF-7	breast:

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs12528284	0.94[CHB][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12661452	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2032544	0.94[CHB][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2032545	0.94[CHB][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs34324183	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35574615	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35798186	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3778380	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3778381	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3778383	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3799579	0.94[CHB][hapmap]
rs3799581	0.94[CHB][hapmap];0.90[EUR][1000 genomes]
rs3799582	0.94[CHB][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3799589	0.94[CHB][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3799590	0.85[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3799591	0.85[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3799592	1.00[CHB][hapmap];0.81[JPT][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3799593	1.00[CHB][hapmap];0.81[JPT][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3799594	0.85[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3799595	0.85[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3799596	1.00[CHB][hapmap];0.88[JPT][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3799599	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3799601	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3823196	0.85[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3823197	1.00[CHB][hapmap];0.81[JPT][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3823198	0.89[CHB][hapmap];0.83[JPT][hapmap];0.87[ASN][1000 genomes]
rs6907098	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6907443	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs763193	0.89[CHB][hapmap]
rs9295356	0.94[CHB][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9347138	0.94[CHB][hapmap]
rs9348149	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9355586	0.85[CEU][hapmap];0.94[CHB][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9356491	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9356493	0.94[CHB][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9356494	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9366031	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9366033	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs960145	0.89[CHB][hapmap];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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	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
4	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:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:166989000-167011400	Weak transcription	Ovary	ovary
2	chr6:166995000-167008400	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr6:166998000-167011200	Weak transcription	Stomach Smooth Muscle	stomach
4	chr6:167002600-167011400	Weak transcription	Right Atrium	heart
5	chr6:167002600-167013200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr6:167003000-167009000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr6:167003000-167010400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr6:167003000-167010800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr6:167003200-167009600	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr6:167003200-167011200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr6:167003200-167011200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr6:167003400-167009000	Weak transcription	Colon Smooth Muscle	Colon
13	chr6:167003600-167008200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr6:167003600-167008200	Weak transcription	NHDF-Ad	bronchial
15	chr6:167003600-167008800	Weak transcription	HMEC	breast
16	chr6:167003600-167010400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr6:167003600-167011600	Weak transcription	Duodenum Smooth Muscle	Duodenum
18	chr6:167003600-167013000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr6:167003800-167008800	Weak transcription	Rectal Smooth Muscle	rectum
20	chr6:167003800-167009000	Weak transcription	Duodenum Mucosa	Duodenum
21	chr6:167004000-167008200	Weak transcription	HSMM	muscle
22	chr6:167004000-167009000	Weak transcription	Brain Hippocampus Middle	brain
23	chr6:167004000-167009200	Weak transcription	Brain Cingulate Gyrus	brain
24	chr6:167004000-167010600	Weak transcription	Fetal Stomach	stomach
25	chr6:167004000-167010600	Weak transcription	Gastric	stomach
26	chr6:167004200-167008800	Weak transcription	Fetal Muscle Leg	muscle
27	chr6:167004200-167009000	Weak transcription	Brain Substantia Nigra	brain
28	chr6:167004200-167010400	Weak transcription	HUVEC	blood vessel
29	chr6:167004200-167010800	Weak transcription	Spleen	Spleen
30	chr6:167004200-167012200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr6:167004400-167009000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr6:167004600-167010800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr6:167004800-167009000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr6:167004800-167009600	Weak transcription	Fetal Muscle Trunk	muscle
35	chr6:167004800-167010400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr6:167004800-167010400	Weak transcription	Brain Anterior Caudate	brain
37	chr6:167004800-167010600	Weak transcription	Esophagus	oesophagus
38	chr6:167005000-167009600	Weak transcription	Brain Angular Gyrus	brain
39	chr6:167005000-167010400	Weak transcription	Pancreas	Pancrea
40	chr6:167005400-167010800	Weak transcription	Cortex derived primary cultured neurospheres	brain
41	chr6:167006000-167008600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr6:167006000-167008800	Weak transcription	Right Ventricle	heart
43	chr6:167006000-167012400	Weak transcription	Skeletal Muscle Male	skeletal muscle
44	chr6:167006200-167009200	Weak transcription	Fetal Heart	heart
45	chr6:167006200-167011400	Weak transcription	Skeletal Muscle Female	skeletal muscle
46	chr6:167006400-167008000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr6:167006400-167008400	Weak transcription	HSMMtube	muscle
48	chr6:167006400-167009200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr6:167006400-167009600	Weak transcription	Lung	lung
50	chr6:167006600-167008000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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