Variant report

Variant	rs12661820
Chromosome Location	chr6:166984656-166984657
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:166982541..166984779-chr6:166986370..166988271,2	K562	blood:

Extended variants
information (count: 11 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs11755586	0.91[CEU][hapmap];0.91[MEX][hapmap];0.83[TSI][hapmap]
rs1543802	0.81[CEU][hapmap]
rs3799609	0.86[CEU][hapmap];0.90[CHB][hapmap];0.90[JPT][hapmap];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3799610	0.89[GIH][hapmap]
rs3799620	0.81[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 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
5	nsv1029530	chr6:166977678-167016052	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv605260	chr6:166984094-167455139	Enhancers Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12661820	PHF10	cis	parietal	SCAN
rs12661820	C6orf208	cis	cerebellum	SCAN

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:166968400-166985800	Weak transcription	Fetal Kidney	kidney
2	chr6:166970800-166986200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr6:166971000-166986000	Weak transcription	Pancreas	Pancrea
4	chr6:166972200-166986000	Weak transcription	Gastric	stomach
5	chr6:166973800-166986000	Weak transcription	Fetal Intestine Small	intestine
6	chr6:166974000-166989600	Weak transcription	Primary T cells from cord blood	blood
7	chr6:166974400-166992400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr6:166974800-166986000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr6:166976400-166988600	Weak transcription	Ovary	ovary
10	chr6:166977800-166985800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr6:166978600-166985800	Weak transcription	Cortex derived primary cultured neurospheres	brain
12	chr6:166978800-166984800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr6:166979000-166984800	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr6:166979000-166985800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr6:166979400-166996600	Weak transcription	Primary neutrophils fromperipheralblood	blood
16	chr6:166979400-166997600	Weak transcription	Stomach Smooth Muscle	stomach
17	chr6:166980000-166985800	Weak transcription	Brain Substantia Nigra	brain
18	chr6:166980000-166986000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr6:166980200-166986200	Weak transcription	Brain Inferior Temporal Lobe	brain
20	chr6:166980400-166986000	Weak transcription	Brain Germinal Matrix	brain
21	chr6:166980600-166984800	Weak transcription	Brain Hippocampus Middle	brain
22	chr6:166980600-166985800	Weak transcription	Brain Angular Gyrus	brain
23	chr6:166980800-166986200	Weak transcription	Right Atrium	heart
24	chr6:166981000-166985800	Weak transcription	Skeletal Muscle Female	skeletal muscle
25	chr6:166981000-166986000	Weak transcription	Brain Anterior Caudate	brain
26	chr6:166981000-166986000	Weak transcription	Brain Cingulate Gyrus	brain
27	chr6:166981200-166992200	Weak transcription	HSMMtube	muscle
28	chr6:166981400-166985600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr6:166981400-166985600	Weak transcription	Osteobl	bone
30	chr6:166981400-166985800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr6:166981400-166986000	Weak transcription	Placenta Amnion	Placenta Amnion
32	chr6:166981400-166986000	Weak transcription	Skeletal Muscle Male	skeletal muscle
33	chr6:166981600-166985400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr6:166981600-166985800	Weak transcription	Fetal Muscle Leg	muscle
35	chr6:166981600-166985800	Weak transcription	Fetal Stomach	stomach
36	chr6:166981600-166985800	Weak transcription	NHDF-Ad	bronchial
37	chr6:166981600-166986000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr6:166981600-166986000	Weak transcription	Right Ventricle	heart
39	chr6:166981600-166986000	Weak transcription	HSMM	muscle
40	chr6:166981800-166985600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr6:166981800-166985800	Weak transcription	Adipose Nuclei	Adipose
42	chr6:166981800-167002400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr6:166982400-166984800	Weak transcription	Muscle Satellite Cultured Cells	--
44	chr6:166982800-166985800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
45	chr6:166983000-166984800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
46	chr6:166983000-166986200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr6:166983000-166986200	Enhancers	NHLF	lung
48	chr6:166983400-166986200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr6:166983800-166986000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr6:166983800-166986000	Weak transcription	Esophagus	oesophagus

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