Variant report

Variant	rs12943181
Chromosome Location	chr17:66424341-66424342
allele	C/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	chr17:66423908-66424354	HepG2	liver:	n/a	n/a
2	POLR2A	chr17:66421619-66424469	K562	blood:	n/a	n/a
3	FOSL2	chr17:66423648-66424383	HepG2	liver:	n/a	chr17:66424013-66424020

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:66285150..66290165-chr17:66423576..66430541,21	MCF-7	breast:
2	chr17:66242241..66245075-chr17:66423885..66426566,2	MCF-7	breast:

Variant related genes	Relation type
MIR635	TF binding region
WIPI1	TF binding region
ENSG00000265100	Chromatin interaction
ENSG00000141337	Chromatin interaction
ENSG00000196704	Chromatin interaction
ENSG00000108932	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs1002446	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11077542	0.87[ASW][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.92[MKK][hapmap];0.82[TSI][hapmap];0.94[YRI][hapmap];0.91[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs11656906	0.87[ASW][hapmap]
rs11870010	0.87[ASW][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.89[YRI][hapmap];0.97[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs12453020	0.82[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.92[MKK][hapmap];0.84[YRI][hapmap];0.91[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs12945490	0.94[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs12946747	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]
rs12947036	0.94[AFR][1000 genomes];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12948224	0.84[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2302782	0.87[ASW][hapmap]
rs2952278	0.87[ASW][hapmap]
rs2952291	0.87[ASW][hapmap]
rs918167	0.87[ASW][hapmap]

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
rs12943181	NOL11	cis	cerebellum	SCAN
rs12943181	CCDC47	cis	parietal	SCAN

Chromatin state (count:116 , 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	chr17:66411600-66427800	Weak transcription	Primary T helper cells PMA-I stimulated	--
5	chr17:66412200-66424800	Weak transcription	Dnd41	blood
6	chr17:66412200-66427800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
7	chr17:66412200-66427800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
8	chr17:66412200-66432000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
9	chr17:66413400-66425000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr17:66413800-66424800	Weak transcription	HSMM	muscle
11	chr17:66414200-66432200	Strong transcription	Primary neutrophils fromperipheralblood	blood
12	chr17:66414400-66427800	Strong transcription	Skeletal Muscle Female	skeletal muscle
13	chr17:66414600-66426800	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr17:66414600-66432400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr17:66414800-66425000	Weak transcription	Primary B cells from cord blood	blood
16	chr17:66415000-66426000	Weak transcription	Fetal Lung	lung
17	chr17:66415400-66424800	Weak transcription	Fetal Heart	heart
18	chr17:66415400-66424800	Weak transcription	GM12878-XiMat	blood
19	chr17:66415400-66428600	Strong transcription	Skeletal Muscle Male	skeletal muscle
20	chr17:66415800-66427400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
21	chr17:66415800-66427800	Strong transcription	Left Ventricle	heart
22	chr17:66415800-66430400	Strong transcription	HSMMtube	muscle
23	chr17:66415800-66431600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr17:66415800-66431800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr17:66415800-66432000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
26	chr17:66415800-66432200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr17:66415800-66432200	Strong transcription	Adipose Nuclei	Adipose
28	chr17:66415800-66432200	Strong transcription	Brain Hippocampus Middle	brain
29	chr17:66415800-66432200	Strong transcription	Duodenum Smooth Muscle	Duodenum
30	chr17:66415800-66432200	Strong transcription	Placenta	Placenta
31	chr17:66415800-66432200	Strong transcription	Monocytes-CD14+_RO01746	blood
32	chr17:66415800-66432400	Strong transcription	Rectal Mucosa Donor 29	rectum
33	chr17:66415800-66433600	Weak transcription	Small Intestine	intestine
34	chr17:66416000-66432200	Strong transcription	Primary monocytes fromperipheralblood	blood
35	chr17:66416000-66432200	Strong transcription	Fetal Muscle Trunk	muscle
36	chr17:66416000-66432200	Strong transcription	Osteobl	bone
37	chr17:66416000-66432400	Strong transcription	Brain Substantia Nigra	brain
38	chr17:66416000-66432400	Strong transcription	Sigmoid Colon	Sigmoid Colon
39	chr17:66416200-66432400	Strong transcription	Rectal Smooth Muscle	rectum
40	chr17:66416200-66432600	Strong transcription	Brain Cingulate Gyrus	brain
41	chr17:66416400-66424400	Strong transcription	Liver	Liver
42	chr17:66416400-66432200	Strong transcription	Colonic Mucosa	Colon
43	chr17:66416600-66432000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr17:66416600-66432200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr17:66416600-66432400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr17:66416800-66431600	Strong transcription	Lung	lung
47	chr17:66416800-66432000	Strong transcription	Stomach Smooth Muscle	stomach
48	chr17:66416800-66432200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
49	chr17:66417000-66431400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr17:66417000-66432000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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