Variant report

Variant	rs4379286
Chromosome Location	chr6:12329292-12329293
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:12313605..12316031-chr6:12327791..12330633,2	MCF-7	breast:
2	chr6:12327141..12329484-chr6:12596719..12598880,2	MCF-7	breast:
3	chr6:12322236..12325054-chr6:12326610..12329434,2	K562	blood:
4	chr6:12297751..12299644-chr6:12328218..12330903,2	MCF-7	breast:
5	chr6:12286691..12293887-chr6:12327157..12336724,21	MCF-7	breast:

Variant related genes	Relation type
ENSG00000078401	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10947948	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10947949	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11753558	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12055484	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17765653	0.84[CHD][hapmap];0.85[JPT][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4711655	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4714383	0.95[CHD][hapmap];0.85[JPT][hapmap];0.83[MEX][hapmap];0.80[TSI][hapmap];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4714384	0.93[CHD][hapmap];0.90[JPT][hapmap];0.82[MEX][hapmap]
rs4714418	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6458187	0.86[EUR][1000 genomes]
rs6458193	0.84[CEU][hapmap];0.81[CHB][hapmap];0.95[JPT][hapmap];0.86[MEX][hapmap];0.91[TSI][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6921790	0.81[CEU][hapmap];0.85[CHB][hapmap];0.94[JPT][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6932390	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9357346	0.88[CEU][hapmap];0.87[CHB][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9369262	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]
rs9381015	0.84[CEU][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9381033	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9381035	0.88[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.81[TSI][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9394741	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[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	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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4379286	NFIL3	trans	cerebellum	SCAN
rs4379286	GMPR	cis	cerebellum	SCAN
rs4379286	RN7SKP293	cis	Artery Tibial	GTEx

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:12324800-12331000	Weak transcription	Pancreas	Pancrea
2	chr6:12325200-12331600	Weak transcription	Duodenum Mucosa	Duodenum
3	chr6:12325200-12332200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr6:12325400-12329600	Enhancers	A549	lung
5	chr6:12325400-12331000	Weak transcription	Fetal Intestine Large	intestine
6	chr6:12325400-12332000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr6:12326200-12329400	Enhancers	iPS-15b Cell Line	embryonic stem cell
8	chr6:12327000-12329600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr6:12327000-12330200	Enhancers	HMEC	breast
10	chr6:12327400-12330000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr6:12327400-12330000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr6:12327400-12334600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr6:12327600-12329400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr6:12327800-12329400	Enhancers	Hela-S3	cervix
15	chr6:12327800-12337000	Enhancers	HepG2	liver
16	chr6:12328000-12335200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
17	chr6:12328400-12329400	Enhancers	Placenta Amnion	Placenta Amnion
18	chr6:12328600-12329400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr6:12328600-12329400	Enhancers	Fetal Thymus	thymus
20	chr6:12328600-12329400	Flanking Active TSS	NHEK	skin
21	chr6:12328600-12329600	Enhancers	Esophagus	oesophagus
22	chr6:12328800-12329400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr6:12328800-12329400	Enhancers	Fetal Intestine Small	intestine
24	chr6:12328800-12334000	Enhancers	Stomach Mucosa	stomach
25	chr6:12328800-12334800	Weak transcription	HUES6 Cell Line	embryonic stem cell
26	chr6:12329000-12329400	Enhancers	Rectal Mucosa Donor 31	rectum
27	chr6:12329000-12330000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr6:12329200-12331600	Weak transcription	iPS-20b Cell Line	embryonic stem cell

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