Variant report

Variant	rs6456092
Chromosome Location	chr6:166957334-166957335
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 11 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs13207398	0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3799631	0.95[CEU][hapmap];0.85[CHB][hapmap];0.97[CHD][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];0.90[TSI][hapmap];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6456091	0.95[CHB][hapmap];0.85[JPT][hapmap];0.94[ASN][1000 genomes]
rs6456093	0.91[CEU][hapmap];0.83[TSI][hapmap];0.88[EUR][1000 genomes]
rs6918886	0.95[CHB][hapmap];1.00[CHD][hapmap];0.85[JPT][hapmap];0.95[ASN][1000 genomes]
rs763186	0.95[CHB][hapmap];0.95[CHD][hapmap];0.92[ASN][1000 genomes]
rs7769210	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9348147	0.90[CHB][hapmap];0.89[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	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6456092	CCR6	cis	cerebellum	SCAN

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:166930400-166957800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr6:166935400-166966400	Weak transcription	NH-A	brain
3	chr6:166944600-166958600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr6:166947400-166969400	Weak transcription	Aorta	Aorta
5	chr6:166949800-166964800	Weak transcription	Fetal Intestine Small	intestine
6	chr6:166950200-166960600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr6:166950800-166958600	Weak transcription	NHDF-Ad	bronchial
8	chr6:166951800-166959000	Weak transcription	Primary neutrophils fromperipheralblood	blood
9	chr6:166952400-166969000	Weak transcription	Psoas Muscle	Psoas
10	chr6:166953000-166957800	Enhancers	iPS-20b Cell Line	embryonic stem cell
11	chr6:166953000-166959000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr6:166953400-166957600	Enhancers	H1 Cell Line	embryonic stem cell
13	chr6:166953400-166964600	Weak transcription	Primary T cells from cord blood	blood
14	chr6:166953400-166967400	Weak transcription	Fetal Lung	lung
15	chr6:166954000-166959000	Enhancers	Fetal Muscle Leg	muscle
16	chr6:166954200-166958200	Enhancers	Fetal Muscle Trunk	muscle
17	chr6:166954200-166965000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr6:166954400-166957800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr6:166954400-166958800	Weak transcription	Fetal Brain Female	brain
20	chr6:166954400-166962000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr6:166954600-166958400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr6:166954600-166959000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr6:166954600-166959600	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr6:166954800-166965000	Weak transcription	Brain Cingulate Gyrus	brain
25	chr6:166955000-166957600	Enhancers	ES-I3 Cell Line	embryonic stem cell
26	chr6:166955000-166959200	Weak transcription	Brain Angular Gyrus	brain
27	chr6:166955000-166959400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr6:166955000-166967000	Weak transcription	Brain Substantia Nigra	brain
29	chr6:166955200-166962400	Weak transcription	Cortex derived primary cultured neurospheres	brain
30	chr6:166955200-166970600	Weak transcription	Pancreas	Pancrea
31	chr6:166955200-166970600	Weak transcription	Sigmoid Colon	Sigmoid Colon
32	chr6:166955400-166958400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
33	chr6:166955800-166959200	Weak transcription	Brain Germinal Matrix	brain
34	chr6:166956000-166957800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr6:166956000-166960200	Weak transcription	Rectal Mucosa Donor 31	rectum
36	chr6:166956000-166962400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr6:166956000-166964000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
38	chr6:166956000-166966400	Weak transcription	Adipose Nuclei	Adipose
39	chr6:166956000-166966600	Weak transcription	Stomach Smooth Muscle	stomach
40	chr6:166956000-166967800	Weak transcription	Duodenum Smooth Muscle	Duodenum
41	chr6:166956000-166969000	Weak transcription	Gastric	stomach
42	chr6:166956200-166957400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
43	chr6:166956200-166957600	Weak transcription	HUES6 Cell Line	embryonic stem cell
44	chr6:166956200-166967400	Weak transcription	Ovary	ovary
45	chr6:166956400-166957600	Enhancers	Left Ventricle	heart
46	chr6:166956400-166959600	Weak transcription	Osteobl	bone
47	chr6:166956400-166966400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr6:166956600-166957400	Enhancers	H9 Cell Line	embryonic stem cell
49	chr6:166956600-166957600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
50	chr6:166956600-166966400	Weak transcription	HMEC	breast

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