Variant report

Variant	rs17080238
Chromosome Location	chr6:151070346-151070347
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs11965555	0.81[EUR][1000 genomes]
rs12664155	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17080212	1.00[ASW][hapmap];1.00[CEU][hapmap];0.85[CHB][hapmap];0.88[GIH][hapmap];0.85[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1968998	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1968999	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs2279628	1.00[CEU][hapmap];0.86[MEX][hapmap];0.82[AMR][1000 genomes]
rs3734408	0.81[EUR][1000 genomes]
rs3734409	0.81[EUR][1000 genomes]
rs3734410	0.81[EUR][1000 genomes]
rs3734411	1.00[CEU][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3734413	0.81[EUR][1000 genomes]
rs4869689	0.85[CEU][hapmap];0.85[JPT][hapmap];0.89[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs4869692	0.83[AMR][1000 genomes]
rs4869693	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4869932	0.85[CEU][hapmap]
rs4869935	1.00[CEU][hapmap]
rs58164449	0.83[EUR][1000 genomes]
rs72570328	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs72570331	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs72570332	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs72570334	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs72570348	0.85[EUR][1000 genomes]
rs72570349	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs72570350	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72570374	0.89[EUR][1000 genomes]
rs7748886	1.00[CEU][hapmap];0.86[MEX][hapmap];0.82[AMR][1000 genomes]
rs7772795	1.00[CEU][hapmap];0.85[JPT][hapmap];0.86[MEX][hapmap];0.84[AMR][1000 genomes]
rs9478787	0.85[JPT][hapmap]
rs9478790	1.00[CEU][hapmap];0.85[JPT][hapmap];0.86[AMR][1000 genomes]
rs9478791	1.00[CEU][hapmap];0.86[MEX][hapmap];0.88[AMR][1000 genomes]
rs9480548	1.00[CEU][hapmap]
rs9480550	1.00[CEU][hapmap]
rs9480551	1.00[CEU][hapmap]
rs9918380	0.82[AMR][1000 genomes];0.83[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	nsv1030326	chr6:150967665-151641372	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	nsv1019919	chr6:151028969-151161789	Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
3	nsv538474	chr6:151028969-151161789	Genic enhancers Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:151042400-151074800	Weak transcription	Fetal Intestine Small	intestine
2	chr6:151042600-151085400	Weak transcription	Esophagus	oesophagus
3	chr6:151055600-151074800	Weak transcription	Fetal Intestine Large	intestine
4	chr6:151055800-151074400	Weak transcription	Fetal Stomach	stomach
5	chr6:151055800-151074800	Weak transcription	Duodenum Mucosa	Duodenum
6	chr6:151056000-151087200	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr6:151058600-151075600	Weak transcription	Thymus	Thymus
8	chr6:151061600-151075000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr6:151061600-151112200	Weak transcription	Right Atrium	heart
10	chr6:151062200-151072000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr6:151062200-151072000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr6:151062400-151074400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr6:151063000-151074600	Weak transcription	Brain Anterior Caudate	brain
14	chr6:151064400-151072400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr6:151064400-151072600	Weak transcription	Fetal Thymus	thymus
16	chr6:151067400-151072000	Weak transcription	Cortex derived primary cultured neurospheres	brain
17	chr6:151067400-151074600	Weak transcription	Left Ventricle	heart
18	chr6:151067400-151074800	Weak transcription	Adipose Nuclei	Adipose
19	chr6:151067400-151075000	Weak transcription	Lung	lung
20	chr6:151067600-151072400	Weak transcription	Brain Substantia Nigra	brain
21	chr6:151068200-151070400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
22	chr6:151068200-151073400	Weak transcription	Fetal Kidney	kidney
23	chr6:151068600-151074400	Weak transcription	Placenta Amnion	Placenta Amnion
24	chr6:151068800-151074000	Strong transcription	Primary B cells from peripheral blood	blood
25	chr6:151069000-151074400	Weak transcription	Fetal Lung	lung
26	chr6:151069200-151070600	Strong transcription	Primary B cells from cord blood	blood
27	chr6:151069600-151070800	Enhancers	Fetal Heart	heart
28	chr6:151070000-151070400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr6:151070200-151070600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
30	chr6:151070200-151070600	Enhancers	Fetal Muscle Trunk	muscle
31	chr6:151070200-151070600	Enhancers	Sigmoid Colon	Sigmoid Colon
32	chr6:151070200-151074600	Weak transcription	Rectal Mucosa Donor 31	rectum

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