Variant report

Variant	rs9478809
Chromosome Location	chr6:151072347-151072348
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:151063005..151064688-chr6:151071263..151072957,2	MCF-7	breast:

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs12662499	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12663819	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12664005	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12664858	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13196740	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13201828	1.00[ASN][1000 genomes]
rs13201855	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13211049	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13211397	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13211603	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13216327	0.93[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17080241	0.88[CEU][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17340521	0.88[CEU][hapmap];0.96[EUR][1000 genomes]
rs34254299	0.82[EUR][1000 genomes]
rs4645433	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56028508	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs57798861	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71570234	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs71570235	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs742636	1.00[GIH][hapmap];0.86[MEX][hapmap];0.84[TSI][hapmap]
rs7453338	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7757414	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7774822	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs997374	1.00[CHB][hapmap];0.94[JPT][hapmap];0.86[ASN][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:37 , 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	chr6:151062400-151074400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr6:151063000-151074600	Weak transcription	Brain Anterior Caudate	brain
12	chr6:151064400-151072400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr6:151064400-151072600	Weak transcription	Fetal Thymus	thymus
14	chr6:151067400-151074600	Weak transcription	Left Ventricle	heart
15	chr6:151067400-151074800	Weak transcription	Adipose Nuclei	Adipose
16	chr6:151067400-151075000	Weak transcription	Lung	lung
17	chr6:151067600-151072400	Weak transcription	Brain Substantia Nigra	brain
18	chr6:151068200-151073400	Weak transcription	Fetal Kidney	kidney
19	chr6:151068600-151074400	Weak transcription	Placenta Amnion	Placenta Amnion
20	chr6:151068800-151074000	Strong transcription	Primary B cells from peripheral blood	blood
21	chr6:151069000-151074400	Weak transcription	Fetal Lung	lung
22	chr6:151070200-151074600	Weak transcription	Rectal Mucosa Donor 31	rectum
23	chr6:151070400-151073600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr6:151070600-151072400	Weak transcription	Primary B cells from cord blood	blood
25	chr6:151070600-151072600	Weak transcription	Sigmoid Colon	Sigmoid Colon
26	chr6:151070600-151074400	Weak transcription	Fetal Muscle Trunk	muscle
27	chr6:151070800-151072400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
28	chr6:151070800-151073600	Weak transcription	Fetal Muscle Leg	muscle
29	chr6:151070800-151074600	Weak transcription	Fetal Heart	heart
30	chr6:151071400-151073200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr6:151071600-151074400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr6:151072000-151073200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr6:151072000-151073600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr6:151072000-151074000	Enhancers	Osteobl	bone
35	chr6:151072000-151074200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr6:151072000-151074400	Enhancers	Cortex derived primary cultured neurospheres	brain
37	chr6:151072000-151075400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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