Variant report

Variant	rs9369262
Chromosome Location	chr6:12332170-12332171
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:12292827..12295303-chr6:12330889..12332793,2	MCF-7	breast:
2	chr6:12331038..12333504-chr6:12480063..12482828,2	MCF-7	breast:
3	chr6:12330604..12333158-chr6:12489739..12491762,2	MCF-7	breast:
4	chr6:12330915..12334155-chr6:12334557..12337652,4	MCF-7	breast:
5	chr6:12317622..12319862-chr6:12331456..12333621,2	MCF-7	breast:
6	chr6:12286921..12289909-chr6:12330691..12332397,2	MCF-7	breast:
7	chr6:12329368..12332356-chr6:12340558..12342942,2	MCF-7	breast:
8	chr6:12286691..12293887-chr6:12327157..12336724,21	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000078401	Chromatin interaction
ENSG00000218893	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs10947948	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10947949	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11753558	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12055484	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17765653	0.91[CEU][hapmap];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs17765682	0.85[ASN][1000 genomes]
rs35198442	0.85[ASN][1000 genomes]
rs4379286	0.88[CEU][hapmap];0.87[CHB][hapmap];0.82[CHD][hapmap];0.95[GIH][hapmap];0.89[LWK][hapmap];0.82[MEX][hapmap];0.87[MKK][hapmap];0.85[TSI][hapmap];0.89[YRI][hapmap];0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4711654	0.83[CEU][hapmap]
rs4711655	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4714383	0.81[CHD][hapmap];0.86[EUR][1000 genomes]
rs4714418	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6458187	0.87[EUR][1000 genomes]
rs6458193	0.95[CEU][hapmap];0.84[TSI][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6921790	0.90[CEU][hapmap];0.81[CHB][hapmap];0.84[EUR][1000 genomes]
rs6932390	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9357346	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9381015	0.95[CEU][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9381033	0.91[CEU][hapmap];0.84[EUR][1000 genomes]
rs9381035	1.00[CEU][hapmap];0.87[CHB][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9394741	0.94[EUR][1000 genomes]
rs9462681	0.80[EUR][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	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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs9369262	GMPR	cis	cerebellum	SCAN
rs9369262	RNF182	cis	parietal	SCAN
rs9369262	NFIL3	trans	cerebellum	SCAN
rs9369262	RN7SKP293	cis	Artery Tibial	GTEx

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:12325200-12332200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
2	chr6:12327400-12334600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr6:12327800-12337000	Enhancers	HepG2	liver
4	chr6:12328000-12335200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
5	chr6:12328800-12334000	Enhancers	Stomach Mucosa	stomach
6	chr6:12328800-12334800	Weak transcription	HUES6 Cell Line	embryonic stem cell
7	chr6:12329400-12332200	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr6:12329400-12334600	Weak transcription	Hela-S3	cervix
9	chr6:12329400-12335400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr6:12329400-12336000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr6:12329400-12336000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr6:12330200-12332200	Weak transcription	NHEK	skin
13	chr6:12330800-12332200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr6:12331000-12332800	Enhancers	Pancreas	Pancrea
15	chr6:12331000-12333000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr6:12331000-12333200	Enhancers	Rectal Mucosa Donor 31	rectum
17	chr6:12331000-12337200	Enhancers	Fetal Intestine Large	intestine
18	chr6:12331000-12337200	Enhancers	Fetal Intestine Small	intestine
19	chr6:12331400-12332800	Enhancers	Liver	Liver
20	chr6:12331400-12332800	Enhancers	Stomach Smooth Muscle	stomach
21	chr6:12331600-12332400	Enhancers	Duodenum Smooth Muscle	Duodenum
22	chr6:12331600-12332600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr6:12331600-12332800	Enhancers	iPS-20b Cell Line	embryonic stem cell
24	chr6:12331600-12332800	Enhancers	Left Ventricle	heart
25	chr6:12331600-12333000	Enhancers	Placenta	Placenta
26	chr6:12331600-12333600	Enhancers	Duodenum Mucosa	Duodenum
27	chr6:12331800-12332200	Enhancers	Aorta	Aorta
28	chr6:12331800-12332200	Flanking Active TSS	A549	lung
29	chr6:12331800-12333000	Enhancers	Adipose Nuclei	Adipose
30	chr6:12332000-12332400	Active TSS	Rectal Mucosa Donor 29	rectum
31	chr6:12332000-12332600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr6:12332000-12332800	Enhancers	ES-I3 Cell Line	embryonic stem cell
33	chr6:12332000-12333800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr6:12332000-12340200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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