Variant report

Variant	rs2343591
Chromosome Location	chr6:166792405-166792406
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	E2F4	chr6:166792309-166792651	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:166747123..166748829-chr6:166792076..166793890,2	K562	blood:

Variant related genes	Relation type
ENSG00000261420	TF binding region
ENSG00000233231	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs1546853	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1546854	0.86[CEU][hapmap];0.93[GIH][hapmap];0.82[TSI][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1546855	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1569459	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1569460	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1569461	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1977049	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1977050	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1977051	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1977052	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1977053	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1977054	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1977056	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2179177	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3734605	1.00[CEU][hapmap];1.00[GIH][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3757194	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3757195	0.95[CEU][hapmap];0.93[GIH][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4305699	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes]
rs4710043	0.90[EUR][1000 genomes]
rs6456078	0.95[CEU][hapmap];1.00[GIH][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6456079	0.95[CEU][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.80[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6456081	0.93[EUR][1000 genomes]
rs6905635	1.00[CEU][hapmap];0.80[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6906844	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6912695	0.95[CEU][hapmap];0.99[EUR][1000 genomes]
rs6918091	0.86[EUR][1000 genomes]
rs6918135	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7449594	0.80[EUR][1000 genomes]
rs7449629	0.95[CEU][hapmap];0.93[GIH][hapmap];0.92[TSI][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7744743	0.95[CEU][hapmap];0.96[EUR][1000 genomes]
rs7752716	0.95[CEU][hapmap];0.92[EUR][1000 genomes]
rs9283865	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9295338	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9295341	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9295342	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9295343	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9295344	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9295345	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9348123	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9348124	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9348125	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9348126	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9355574	0.91[CEU][hapmap];1.00[GIH][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes]
rs9355575	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9356482	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9356483	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9364845	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9364846	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9364847	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9364848	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9366009	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9366010	0.83[AMR][1000 genomes];0.85[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	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	esv3376653	chr6:166783590-166798116	Active TSS Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2343591	C6orf118	cis	cerebellum	SCAN

Chromatin state (count:70 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:166773200-166794600	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr6:166774800-166795000	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr6:166775000-166793800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr6:166775800-166794800	Weak transcription	Primary hematopoietic stem cells	blood
5	chr6:166777400-166795400	Weak transcription	Gastric	stomach
6	chr6:166778200-166792800	Weak transcription	Aorta	Aorta
7	chr6:166778200-166794600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
8	chr6:166778200-166795000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr6:166778400-166792600	Weak transcription	Lung	lung
10	chr6:166778400-166794600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
11	chr6:166778400-166794600	Weak transcription	Fetal Intestine Small	intestine
12	chr6:166778400-166794600	Weak transcription	Stomach Smooth Muscle	stomach
13	chr6:166778400-166794800	Weak transcription	Fetal Stomach	stomach
14	chr6:166778400-166795000	Weak transcription	Colonic Mucosa	Colon
15	chr6:166778600-166794600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr6:166778600-166794600	Weak transcription	Colon Smooth Muscle	Colon
17	chr6:166779200-166793400	Weak transcription	K562	blood
18	chr6:166779400-166794600	Weak transcription	HSMM	muscle
19	chr6:166779400-166794800	Weak transcription	Muscle Satellite Cultured Cells	--
20	chr6:166779600-166792800	Weak transcription	Ovary	ovary
21	chr6:166779600-166794600	Weak transcription	Brain Angular Gyrus	brain
22	chr6:166779600-166794600	Weak transcription	Brain Cingulate Gyrus	brain
23	chr6:166779600-166794600	Weak transcription	Brain Substantia Nigra	brain
24	chr6:166779600-166794600	Weak transcription	Thymus	Thymus
25	chr6:166779600-166794800	Weak transcription	Fetal Intestine Large	intestine
26	chr6:166779800-166793200	Weak transcription	Brain Anterior Caudate	brain
27	chr6:166779800-166794400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr6:166779800-166794600	Weak transcription	NH-A	brain
29	chr6:166780400-166793200	Weak transcription	Adipose Nuclei	Adipose
30	chr6:166780400-166794600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr6:166780600-166794400	Weak transcription	Rectal Mucosa Donor 29	rectum
32	chr6:166780600-166794600	Weak transcription	Primary T helper cells fromperipheralblood	blood
33	chr6:166780600-166794600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
34	chr6:166780600-166794600	Weak transcription	Fetal Lung	lung
35	chr6:166780600-166794800	Weak transcription	Brain Inferior Temporal Lobe	brain
36	chr6:166780600-166795400	Weak transcription	Sigmoid Colon	Sigmoid Colon
37	chr6:166780800-166794600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr6:166780800-166794600	Weak transcription	Primary T cells from cord blood	blood
39	chr6:166780800-166794600	Weak transcription	HSMMtube	muscle
40	chr6:166782600-166794400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr6:166782600-166794600	Weak transcription	Rectal Mucosa Donor 31	rectum
42	chr6:166782600-166794600	Weak transcription	Monocytes-CD14+_RO01746	blood
43	chr6:166782600-166794800	Weak transcription	Primary monocytes fromperipheralblood	blood
44	chr6:166782600-166794800	Weak transcription	Fetal Thymus	thymus
45	chr6:166782600-166795000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
46	chr6:166783000-166792800	Weak transcription	Skeletal Muscle Male	skeletal muscle
47	chr6:166783600-166794600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
48	chr6:166783600-166794600	Weak transcription	Brain Hippocampus Middle	brain
49	chr6:166783800-166794800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr6:166784000-166793400	Weak transcription	Dnd41	blood

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