Variant report

Variant	rs4142117
Chromosome Location	chr6:39392718-39392719
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	chr6:39388076..39390202-chr6:39391495..39393713,2	K562	blood:
2	chr6:39387298..39389611-chr6:39391657..39393931,2	MCF-7	breast:

Extended variants
information (count: 38 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10807207	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs10947809	0.83[ASW][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.96[LWK][hapmap];0.87[MKK][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs10947810	0.94[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.83[MEX][hapmap];0.88[MKK][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs10947811	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs1106961	0.95[CHB][hapmap];0.84[ASN][1000 genomes]
rs12527811	1.00[CHB][hapmap];0.97[CHD][hapmap];0.91[ASN][1000 genomes]
rs1328383	0.95[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs1328388	0.94[CHB][hapmap];0.92[JPT][hapmap];0.86[ASN][1000 genomes]
rs1328389	0.95[CHB][hapmap];0.90[CHD][hapmap];0.92[JPT][hapmap];0.92[ASN][1000 genomes]
rs1328390	0.88[YRI][hapmap];0.93[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs1887713	0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs1999045	0.95[CHB][hapmap];0.82[CHD][hapmap];0.84[ASN][1000 genomes]
rs4142118	0.95[CHB][hapmap];0.86[ASN][1000 genomes]
rs4392720	0.94[CHB][hapmap];0.85[JPT][hapmap];0.87[ASN][1000 genomes]
rs4714250	1.00[CHB][hapmap];0.90[ASN][1000 genomes]
rs4714251	1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];0.92[ASN][1000 genomes]
rs6458114	0.81[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs6458115	1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[JPT][hapmap];0.94[MEX][hapmap];0.82[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs6900629	0.88[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[JPT][hapmap];1.00[LWK][hapmap];0.88[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs6908396	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs72850620	0.84[ASN][1000 genomes]
rs7759557	0.95[CHB][hapmap];0.90[CHD][hapmap];0.88[ASN][1000 genomes]
rs9367004	0.89[CHB][hapmap];0.84[CHD][hapmap];0.84[ASN][1000 genomes]
rs9367005	0.95[CHB][hapmap];0.84[ASN][1000 genomes]
rs9367006	1.00[CHB][hapmap];0.97[CHD][hapmap];0.85[GIH][hapmap];0.93[ASN][1000 genomes]
rs9369114	0.91[CEU][hapmap];0.95[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs9380860	0.85[ASN][1000 genomes]
rs9394591	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.85[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9394592	0.81[CEU][hapmap]
rs9462543	1.00[CHB][hapmap];0.97[CHD][hapmap];0.92[ASN][1000 genomes]
rs9471089	0.84[ASN][1000 genomes]
rs9471090	0.91[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs9471092	0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs9471097	1.00[CHB][hapmap];0.92[JPT][hapmap];0.97[ASN][1000 genomes]
rs9471098	1.00[CHB][hapmap];0.93[CHD][hapmap];0.92[JPT][hapmap];0.97[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	nsv830645	chr6:39227601-39408310	Enhancers Weak transcription Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv533806	chr6:39270073-39397337	Enhancers Bivalent Enhancer Weak transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv885822	chr6:39327708-39721216	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4142117	LOC221442	cis	cerebellum	SCAN
rs4142117	TAS2R5	trans	parietal	SCAN

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:39384200-39393200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr6:39385000-39396400	Weak transcription	HUES64 Cell Line	embryonic stem cell
3	chr6:39385200-39398800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr6:39385400-39393200	Weak transcription	NHEK	skin
5	chr6:39387600-39393600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr6:39387800-39392800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr6:39387800-39396400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
8	chr6:39389000-39393000	Weak transcription	Brain Angular Gyrus	brain
9	chr6:39389000-39393200	Weak transcription	Fetal Lung	lung
10	chr6:39389000-39398000	Weak transcription	Duodenum Smooth Muscle	Duodenum
11	chr6:39389400-39393200	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr6:39389400-39393600	Weak transcription	Brain Cingulate Gyrus	brain
13	chr6:39389400-39398200	Weak transcription	Rectal Smooth Muscle	rectum
14	chr6:39389800-39392800	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr6:39389800-39392800	Weak transcription	Brain Substantia Nigra	brain
16	chr6:39389800-39393800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr6:39390200-39393600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr6:39390200-39394000	Weak transcription	Psoas Muscle	Psoas
19	chr6:39390400-39393200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr6:39390400-39393400	Weak transcription	Colon Smooth Muscle	Colon
21	chr6:39390400-39393600	Weak transcription	Brain Hippocampus Middle	brain
22	chr6:39390400-39399000	Weak transcription	Stomach Mucosa	stomach
23	chr6:39390600-39392800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr6:39390600-39393200	Weak transcription	Brain Anterior Caudate	brain
25	chr6:39390600-39393200	Weak transcription	Fetal Muscle Leg	muscle
26	chr6:39390600-39398800	Weak transcription	Lung	lung
27	chr6:39390800-39392800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr6:39390800-39393400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr6:39390800-39395400	Weak transcription	Skeletal Muscle Female	skeletal muscle
30	chr6:39391000-39393800	Weak transcription	Stomach Smooth Muscle	stomach
31	chr6:39391000-39396600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr6:39391200-39393200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr6:39392200-39395600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr6:39392200-39397800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr6:39392400-39392800	Enhancers	HSMMtube	muscle
36	chr6:39392400-39395000	Enhancers	NHDF-Ad	bronchial
37	chr6:39392600-39393400	Enhancers	Sigmoid Colon	Sigmoid Colon
38	chr6:39392600-39393600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr6:39392600-39396600	Weak transcription	Spleen	Spleen
40	chr6:39392600-39397200	Enhancers	HMEC	breast

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