Variant report

Variant	rs12946747
Chromosome Location	chr17:66422158-66422159
allele	A/G
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	POLR2A	chr17:66421619-66424469	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr17:66286164..66288959-chr17:66420200..66423331,5	MCF-7	breast:
2	chr17:66285633..66288750-chr17:66421298..66423437,3	MCF-7	breast:
3	chr17:66420335..66422992-chr17:66429245..66432195,3	K562	blood:
4	chr17:66421750..66423706-chr17:66426092..66428562,3	MCF-7	breast:

Variant related genes	Relation type
MIR635	TF binding region
ENSG00000141337	Chromatin interaction
ENSG00000108932	Chromatin interaction
ENSG00000070540	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs1002446	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.90[TSI][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11077542	0.87[ASW][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11870010	0.87[ASW][hapmap];0.80[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.83[EUR][1000 genomes]
rs12453020	1.00[ASW][hapmap];0.82[CEU][hapmap];0.82[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.81[YRI][hapmap];0.83[AFR][1000 genomes]
rs12943181	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.82[MKK][hapmap];0.90[TSI][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12945490	0.83[EUR][1000 genomes]
rs12947036	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12948224	0.94[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv833523	chr17:66343323-66510461	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	31 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12946747	NOL11	cis	cerebellum	SCAN
rs12946747	CCDC47	cis	parietal	SCAN

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:66410200-66432200	Weak transcription	Primary B cells from peripheral blood	blood
2	chr17:66410400-66452400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr17:66410600-66427800	Weak transcription	HMEC	breast
4	chr17:66411400-66422400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr17:66411600-66427800	Weak transcription	Primary T helper cells PMA-I stimulated	--
6	chr17:66412200-66424800	Weak transcription	Dnd41	blood
7	chr17:66412200-66427800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
8	chr17:66412200-66427800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
9	chr17:66412200-66432000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
10	chr17:66413400-66425000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr17:66413800-66424800	Weak transcription	HSMM	muscle
12	chr17:66414200-66432200	Strong transcription	Primary neutrophils fromperipheralblood	blood
13	chr17:66414400-66427800	Strong transcription	Skeletal Muscle Female	skeletal muscle
14	chr17:66414600-66426800	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr17:66414600-66432400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr17:66414800-66425000	Weak transcription	Primary B cells from cord blood	blood
17	chr17:66415000-66426000	Weak transcription	Fetal Lung	lung
18	chr17:66415400-66423800	Weak transcription	Fetal Intestine Large	intestine
19	chr17:66415400-66424800	Weak transcription	Fetal Heart	heart
20	chr17:66415400-66424800	Weak transcription	GM12878-XiMat	blood
21	chr17:66415400-66428600	Strong transcription	Skeletal Muscle Male	skeletal muscle
22	chr17:66415800-66427400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
23	chr17:66415800-66427800	Strong transcription	Left Ventricle	heart
24	chr17:66415800-66430400	Strong transcription	HSMMtube	muscle
25	chr17:66415800-66431600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr17:66415800-66431800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr17:66415800-66432000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
28	chr17:66415800-66432200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr17:66415800-66432200	Strong transcription	Adipose Nuclei	Adipose
30	chr17:66415800-66432200	Strong transcription	Brain Hippocampus Middle	brain
31	chr17:66415800-66432200	Strong transcription	Duodenum Smooth Muscle	Duodenum
32	chr17:66415800-66432200	Strong transcription	Placenta	Placenta
33	chr17:66415800-66432200	Strong transcription	Monocytes-CD14+_RO01746	blood
34	chr17:66415800-66432400	Strong transcription	Rectal Mucosa Donor 29	rectum
35	chr17:66415800-66433600	Weak transcription	Small Intestine	intestine
36	chr17:66416000-66432200	Strong transcription	Primary monocytes fromperipheralblood	blood
37	chr17:66416000-66432200	Strong transcription	Fetal Muscle Trunk	muscle
38	chr17:66416000-66432200	Strong transcription	Osteobl	bone
39	chr17:66416000-66432400	Strong transcription	Brain Substantia Nigra	brain
40	chr17:66416000-66432400	Strong transcription	Sigmoid Colon	Sigmoid Colon
41	chr17:66416200-66432400	Strong transcription	Rectal Smooth Muscle	rectum
42	chr17:66416200-66432600	Strong transcription	Brain Cingulate Gyrus	brain
43	chr17:66416400-66422200	Strong transcription	HepG2	liver
44	chr17:66416400-66424400	Strong transcription	Liver	Liver
45	chr17:66416400-66432200	Strong transcription	Colonic Mucosa	Colon
46	chr17:66416600-66432000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr17:66416600-66432200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr17:66416600-66432400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr17:66416800-66431600	Strong transcription	Lung	lung
50	chr17:66416800-66432000	Strong transcription	Stomach Smooth Muscle	stomach

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