Variant report

Variant	rs9475687
Chromosome Location	chr6:56231402-56231403
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:56227775..56231675-chr6:56232771..56236094,3	K562	blood:
2	chr6:56225017..56229279-chr6:56229711..56233671,3	MCF-7	breast:
3	chr6:56230309..56231813-chr6:56301567..56303735,2	MCF-7	breast:

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs12199257	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12204179	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12204391	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12209253	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1543350	0.81[JPT][hapmap]
rs17224911	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17224995	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17225023	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17225519	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MKK][hapmap];0.95[TSI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17225591	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17823397	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17823553	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1883600	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2017390	0.81[JPT][hapmap]
rs2206535	0.81[JPT][hapmap]
rs3950165	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60268580	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6459154	0.89[CEU][hapmap];0.81[JPT][hapmap];0.89[MEX][hapmap];0.85[TSI][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6899968	0.81[JPT][hapmap]
rs6903698	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6908736	0.95[CEU][hapmap];0.90[JPT][hapmap];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6929337	1.00[CEU][hapmap];0.90[JPT][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6929994	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6938343	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7452915	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9349819	0.81[JPT][hapmap]
rs9370524	0.90[JPT][hapmap]
rs9382622	0.81[JPT][hapmap]
rs9464380	1.00[CEU][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9464381	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9475677	0.95[CEU][hapmap];0.90[JPT][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9475678	0.95[CEU][hapmap];0.81[JPT][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9475679	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9475680	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9475682	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9475688	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9986501	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv491933	chr6:56177722-57171010	Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:56221600-56233200	Weak transcription	NHLF	lung
2	chr6:56225200-56234800	Weak transcription	Brain Hippocampus Middle	brain
3	chr6:56225200-56235200	Weak transcription	Brain Cingulate Gyrus	brain
4	chr6:56225200-56235200	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr6:56225800-56233200	Enhancers	HUVEC	blood vessel
6	chr6:56227200-56234800	Enhancers	Hela-S3	cervix
7	chr6:56228600-56232400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr6:56228600-56232800	Enhancers	Breast Myoepithelial Primary Cells	Breast
9	chr6:56229200-56231600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr6:56229200-56232200	Enhancers	Colon Smooth Muscle	Colon
11	chr6:56229200-56236200	Weak transcription	Left Ventricle	heart
12	chr6:56229600-56235000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr6:56229600-56237800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr6:56229800-56232400	Enhancers	Fetal Stomach	stomach
15	chr6:56230000-56235000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr6:56230000-56235000	Weak transcription	HSMMtube	muscle
17	chr6:56230200-56232600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr6:56230200-56233400	Weak transcription	Muscle Satellite Cultured Cells	--
19	chr6:56230200-56234400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr6:56230200-56234600	Weak transcription	HSMM	muscle
21	chr6:56230200-56235000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr6:56230400-56234600	Weak transcription	Pancreatic Islets	Pancreatic Islet
23	chr6:56230600-56234600	Weak transcription	NH-A	brain
24	chr6:56231000-56231600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr6:56231000-56231600	Enhancers	Fetal Muscle Leg	muscle
26	chr6:56231000-56231600	Enhancers	Psoas Muscle	Psoas
27	chr6:56231000-56231600	Enhancers	Right Ventricle	heart
28	chr6:56231000-56231800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr6:56231000-56231800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr6:56231000-56231800	Enhancers	Rectal Smooth Muscle	rectum
31	chr6:56231000-56232400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
32	chr6:56231000-56232400	Enhancers	Fetal Lung	lung
33	chr6:56231000-56235000	Weak transcription	Duodenum Smooth Muscle	Duodenum
34	chr6:56231000-56238000	Enhancers	Adipose Nuclei	Adipose
35	chr6:56231000-56238000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
36	chr6:56231200-56233800	Weak transcription	HMEC	breast
37	chr6:56231200-56233800	Weak transcription	NHEK	skin
38	chr6:56231200-56234400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr6:56231200-56234800	Weak transcription	NHDF-Ad	bronchial
40	chr6:56231200-56235000	Weak transcription	Right Atrium	heart
41	chr6:56231200-56235200	Weak transcription	Fetal Heart	heart
42	chr6:56231200-56235800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr6:56231400-56232400	Enhancers	Fetal Kidney	kidney
44	chr6:56231400-56234800	Enhancers	HepG2	liver
45	chr6:56231400-56235000	Weak transcription	Stomach Smooth Muscle	stomach

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