Variant report

Variant	rs6932390
Chromosome Location	chr6:12340034-12340035
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 24 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10947948	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10947949	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11753558	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12055484	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17765653	0.86[CEU][hapmap];0.84[EUR][1000 genomes]
rs17765682	0.85[ASN][1000 genomes]
rs35198442	0.85[ASN][1000 genomes]
rs4379286	0.84[CEU][hapmap];0.87[CHB][hapmap];0.82[CHD][hapmap];0.95[GIH][hapmap];0.82[MEX][hapmap];0.85[TSI][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4711655	0.84[EUR][1000 genomes]
rs4714383	0.82[CHD][hapmap];0.85[EUR][1000 genomes]
rs4714418	0.81[EUR][1000 genomes]
rs6458187	0.86[EUR][1000 genomes]
rs6458193	0.91[CEU][hapmap];0.84[TSI][hapmap];0.93[EUR][1000 genomes]
rs6921790	0.85[CEU][hapmap];0.81[CHB][hapmap];0.84[EUR][1000 genomes]
rs9357346	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9369262	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9381015	0.91[CEU][hapmap];0.93[EUR][1000 genomes]
rs9381033	0.86[CEU][hapmap];0.84[EUR][1000 genomes]
rs9381035	0.95[CEU][hapmap];0.87[CHB][hapmap];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9394741	0.93[EUR][1000 genomes]
rs9462681	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9462684	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv508394	chr6:12285464-12386745	Strong transcription Genic enhancers Weak transcription Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
2	nsv528681	chr6:12340034-12362219	Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs6932390	NFIL3	trans	cerebellum	SCAN
rs6932390	RN7SKP293	cis	Artery Tibial	GTEx
rs6932390	RNF182	cis	parietal	SCAN
rs6932390	GMPR	cis	cerebellum	SCAN

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:12332000-12340200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr6:12332200-12344000	Weak transcription	Aorta	Aorta
3	chr6:12332600-12340400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr6:12335000-12342000	Weak transcription	Primary monocytes fromperipheralblood	blood
5	chr6:12335000-12342000	Weak transcription	Monocytes-CD14+_RO01746	blood
6	chr6:12336000-12343400	Weak transcription	Fetal Kidney	kidney
7	chr6:12336800-12340200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr6:12336800-12341600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr6:12336800-12341800	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr6:12336800-12342000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr6:12336800-12342000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr6:12337000-12340200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr6:12337000-12341400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr6:12337000-12341600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr6:12337000-12341600	Weak transcription	Stomach Mucosa	stomach
16	chr6:12337000-12341800	Weak transcription	HUES64 Cell Line	embryonic stem cell
17	chr6:12337200-12341400	Weak transcription	HUES48 Cell Line	embryonic stem cell
18	chr6:12337200-12342000	Weak transcription	Hela-S3	cervix
19	chr6:12337200-12348600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr6:12338200-12343000	Enhancers	Liver	Liver
21	chr6:12338200-12345800	Enhancers	Fetal Intestine Small	intestine
22	chr6:12338600-12342600	Enhancers	A549	lung
23	chr6:12338800-12340600	Enhancers	Duodenum Mucosa	Duodenum
24	chr6:12338800-12345800	Enhancers	Rectal Mucosa Donor 31	rectum
25	chr6:12339000-12346200	Enhancers	Fetal Intestine Large	intestine
26	chr6:12339400-12340400	Weak transcription	NHEK	skin
27	chr6:12339600-12340200	Enhancers	Rectal Mucosa Donor 29	rectum
28	chr6:12339600-12340200	Enhancers	Small Intestine	intestine
29	chr6:12339800-12340600	Enhancers	Colonic Mucosa	Colon
30	chr6:12339800-12340600	Enhancers	Sigmoid Colon	Sigmoid Colon
31	chr6:12339800-12340800	Flanking Active TSS	HepG2	liver
32	chr6:12339800-12341000	Enhancers	Pancreas	Pancrea
33	chr6:12340000-12340200	Enhancers	HUES6 Cell Line	embryonic stem cell
34	chr6:12340000-12340400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr6:12340000-12340400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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