Variant report

Variant	rs1543802
Chromosome Location	chr6:166972873-166972874
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	chr6:166970917..166973753-chr6:166974346..166977201,2	K562	blood:

Extended variants
information (count: 15 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs12661820	0.81[CEU][hapmap]
rs2032546	1.00[CHB][hapmap];0.83[JPT][hapmap];0.93[ASN][1000 genomes]
rs3778402	1.00[CHB][hapmap];0.83[JPT][hapmap];0.89[ASN][1000 genomes]
rs3778404	1.00[CHB][hapmap];0.83[JPT][hapmap];0.93[ASN][1000 genomes]
rs3799612	1.00[CHB][hapmap];0.97[CHD][hapmap];0.83[JPT][hapmap];0.89[ASN][1000 genomes]
rs3799613	1.00[CHB][hapmap];0.97[CHD][hapmap];0.83[JPT][hapmap];0.89[ASN][1000 genomes]
rs3799620	1.00[ASW][hapmap];1.00[CEU][hapmap];0.83[CHB][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.94[LWK][hapmap];0.96[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3799630	1.00[CHB][hapmap];0.97[CHD][hapmap];0.83[JPT][hapmap];0.86[ASN][1000 genomes]
rs9348148	0.94[CHB][hapmap];0.83[JPT][hapmap];0.93[ASN][1000 genomes]
rs9355584	0.81[ASW][hapmap];0.83[LWK][hapmap];0.87[MKK][hapmap];0.94[YRI][hapmap];0.88[AFR][1000 genomes]
rs9459695	0.88[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 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	nsv886941	chr6:166907173-166996991	Strong transcription Weak transcription Genic enhancers Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA	5 gene(s)	inside rSNPs	diseases
4	nsv5592	chr6:166958317-167002951	Weak transcription Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1543802	C6orf208	cis	cerebellum	SCAN

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:166966000-166973600	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr6:166966000-166974200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr6:166966200-166978000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr6:166968400-166985800	Weak transcription	Fetal Kidney	kidney
5	chr6:166968800-166973800	Enhancers	HMEC	breast
6	chr6:166969000-166973800	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr6:166969000-166974000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
8	chr6:166969400-166978800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr6:166970200-166976200	Weak transcription	Right Ventricle	heart
10	chr6:166970800-166974000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr6:166970800-166979800	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr6:166970800-166986200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr6:166971000-166973200	Enhancers	HSMM	muscle
14	chr6:166971000-166973400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr6:166971000-166973400	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr6:166971000-166973400	Weak transcription	Ovary	ovary
17	chr6:166971000-166974000	Enhancers	Osteobl	bone
18	chr6:166971000-166974800	Weak transcription	Psoas Muscle	Psoas
19	chr6:166971000-166974800	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr6:166971000-166975600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr6:166971000-166976600	Weak transcription	H1 Cell Line	embryonic stem cell
22	chr6:166971000-166986000	Weak transcription	Pancreas	Pancrea
23	chr6:166971200-166973000	Enhancers	HSMMtube	muscle
24	chr6:166971400-166980200	Weak transcription	Brain Anterior Caudate	brain
25	chr6:166972000-166973400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
26	chr6:166972000-166973400	Weak transcription	Brain Cingulate Gyrus	brain
27	chr6:166972200-166976200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr6:166972200-166976200	Weak transcription	Right Atrium	heart
29	chr6:166972200-166979600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr6:166972200-166986000	Weak transcription	Gastric	stomach
31	chr6:166972400-166973000	Weak transcription	NHDF-Ad	bronchial
32	chr6:166972400-166973800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr6:166972400-166974000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr6:166972400-166974000	Weak transcription	Esophagus	oesophagus
35	chr6:166972400-166974600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr6:166972400-166974600	Weak transcription	Fetal Stomach	stomach
37	chr6:166972400-166974600	Weak transcription	Skeletal Muscle Female	skeletal muscle
38	chr6:166972400-166974800	Weak transcription	Left Ventricle	heart
39	chr6:166972400-166974800	Weak transcription	NHLF	lung
40	chr6:166972400-166979200	Weak transcription	NHEK	skin
41	chr6:166972600-166973000	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr6:166972600-166973800	ZNF genes & repeats	Fetal Muscle Leg	muscle
43	chr6:166972600-166976400	Weak transcription	HUVEC	blood vessel
44	chr6:166972800-166973000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr6:166972800-166973000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr6:166972800-166973000	ZNF genes & repeats	Spleen	Spleen
47	chr6:166972800-166973400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr6:166972800-166973800	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr6:166972800-166973800	ZNF genes & repeats	Primary neutrophils fromperipheralblood	blood

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