Variant report

Variant	rs36014129
Chromosome Location	chr6:25884519-25884520
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	MYC	chr6:25884197-25884661	MCF10A-Er-Src	breast:	n/a	chr6:25884230-25884239
2	CREB1	chr6:25884337-25884554	A549	lung:	n/a	n/a
3	FOS	chr6:25884217-25884574	MCF10A-Er-Src	breast:	n/a	chr6:25884388-25884397
4	STAT3	chr6:25884284-25884560	MCF10A-Er-Src	breast:	n/a	chr6:25884389-25884397
5	E2F4	chr6:25883813-25884695	MCF10A-Er-Src	breast:	n/a	n/a
6	NR3C1	chr6:25884177-25884609	A549	lung:	n/a	chr6:25884518-25884544 chr6:25884522-25884540
7	CEBPB	chr6:25884214-25884665	Hela-S3	cervix:	n/a	n/a
8	TCF12	chr6:25884184-25884682	SK-N-SH	brain:	n/a	n/a
9	STAT3	chr6:25883898-25884602	MCF10A-Er-Src	breast:	n/a	chr6:25884389-25884397
10	EP300	chr6:25884110-25884633	A549	lung:	n/a	chr6:25884390-25884399 chr6:25884228-25884242
11	NR3C1	chr6:25883815-25884686	A549	lung:	n/a	chr6:25884014-25884030 chr6:25884015-25884029 chr6:25884518-25884544 chr6:25884014-25884030 chr6:25884015-25884029 chr6:25884522-25884540 chr6:25884014-25884030 chr6:25884013-25884031 chr6:25884014-25884030 chr6:25884012-25884033
12	NR3C1	chr6:25884278-25884608	A549	lung:	n/a	chr6:25884518-25884544 chr6:25884522-25884540
13	JUND	chr6:25884239-25884597	A549	lung:	n/a	chr6:25884388-25884397
14	EP300	chr6:25884230-25884561	A549	lung:	n/a	chr6:25884390-25884399
15	FOSL2	chr6:25884095-25884657	A549	lung:	n/a	chr6:25884388-25884397
16	NR3C1	chr6:25884142-25884710	A549	lung:	n/a	chr6:25884518-25884544 chr6:25884522-25884540
17	FOS	chr6:25883879-25884760	MCF10A-Er-Src	breast:	n/a	chr6:25884388-25884397
18	GATA3	chr6:25884209-25884795	A549	lung:	n/a	n/a
19	SP1	chr6:25884219-25884643	A549	lung:	n/a	n/a
20	CEBPB	chr6:25884191-25884632	A549	lung:	n/a	n/a
21	NR3C1	chr6:25884207-25884665	A549	lung:	n/a	chr6:25884518-25884544 chr6:25884522-25884540
22	FOS	chr6:25883789-25884617	MCF10A-Er-Src	breast:	n/a	chr6:25884388-25884397
23	CEBPB	chr6:25883855-25884682	A549	lung:	n/a	n/a
24	CEBPB	chr6:25884175-25884698	HepG2	liver:	n/a	n/a
25	NR3C1	chr6:25884238-25884610	A549	lung:	n/a	chr6:25884518-25884544 chr6:25884522-25884540
26	STAT3	chr6:25884331-25884583	MCF10A-Er-Src	breast:	n/a	chr6:25884389-25884397
27	CEBPB	chr6:25884122-25884720	A549	lung:	n/a	n/a
28	TCF12	chr6:25884065-25884781	A549	lung:	n/a	n/a
29	FOS	chr6:25884188-25884658	MCF10A-Er-Src	breast:	n/a	chr6:25884388-25884397
30	MYC	chr6:25884202-25884657	MCF10A-Er-Src	breast:	n/a	chr6:25884230-25884239
31	STAT3	chr6:25884247-25884529	MCF10A-Er-Src	breast:	n/a	chr6:25884389-25884397
32	SP1	chr6:25884128-25884647	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:25879537..25882232-chr6:25883181..25884955,2	K562	blood:
2	chr6:25878620..25881037-chr6:25883177..25884681,2	K562	blood:
3	chr6:25775506..25777112-chr6:25883078..25885992,2	MCF-7	breast:

Variant related genes	Relation type
HIST1H2APS2	TF binding region
SLC17A3	TF binding region

Extended variants
information (count: 46 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs13191445	0.94[EUR][1000 genomes]
rs13191776	0.80[EUR][1000 genomes]
rs13192713	0.80[EUR][1000 genomes]
rs13193424	0.80[EUR][1000 genomes]
rs13195279	0.80[EUR][1000 genomes]
rs13198474	0.90[EUR][1000 genomes]
rs13201341	0.81[EUR][1000 genomes]
rs13202371	0.80[EUR][1000 genomes]
rs13202592	0.94[EUR][1000 genomes]
rs13202688	0.94[EUR][1000 genomes]
rs13207673	0.80[EUR][1000 genomes]
rs13210041	0.87[EUR][1000 genomes]
rs13211947	0.92[EUR][1000 genomes]
rs13212534	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13220488	0.80[EUR][1000 genomes]
rs17526722	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17528178	0.94[EUR][1000 genomes]
rs17586553	0.80[EUR][1000 genomes]
rs17586784	0.80[EUR][1000 genomes]
rs17587226	0.83[EUR][1000 genomes]
rs2051539	0.80[EUR][1000 genomes]
rs34043431	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs34116162	0.80[EUR][1000 genomes]
rs34233736	0.80[EUR][1000 genomes]
rs34888489	0.83[EUR][1000 genomes]
rs35050608	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs35069699	0.80[EUR][1000 genomes]
rs35169013	0.80[EUR][1000 genomes]
rs35506517	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs35778245	0.80[EUR][1000 genomes]
rs3884025	0.98[EUR][1000 genomes]
rs41266779	0.94[EUR][1000 genomes]
rs55912630	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs67491322	0.83[EUR][1000 genomes]
rs67554133	0.85[EUR][1000 genomes]
rs67844427	0.80[EUR][1000 genomes]
rs68194335	0.89[EUR][1000 genomes]
rs71557312	0.94[EUR][1000 genomes]
rs9467626	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1029920	chr6:25638507-26585842	Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Enhancers Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS Genic enhancers Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1215 gene(s)	inside rSNPs	diseases
2	nsv538162	chr6:25638507-26585842	Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1215 gene(s)	inside rSNPs	diseases
3	nsv427747	chr6:25641380-25908218	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
4	nsv1030351	chr6:25813178-26352046	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1189 gene(s)	inside rSNPs	diseases
5	nsv1023453	chr6:25853830-26528250	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1201 gene(s)	inside rSNPs	diseases
6	nsv1025237	chr6:25874326-26280867	Flanking Active TSS Active TSS Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1166 gene(s)	inside rSNPs	diseases
7	nsv538163	chr6:25874326-26280867	Enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1166 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs36014129	BTN3A2///BTN3A3	Cis_1M	lymphoblastoid	RTeQTL
rs36014129	BTN3A2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:25883800-25884600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
2	chr6:25883800-25884600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr6:25883800-25884600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr6:25883800-25884800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr6:25883800-25884800	Enhancers	HMEC	breast
6	chr6:25883800-25884800	Enhancers	HSMM	muscle
7	chr6:25883800-25885000	Enhancers	Liver	Liver
8	chr6:25883800-25885400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr6:25884000-25885000	Enhancers	Osteobl	bone
10	chr6:25884200-25884600	Enhancers	HepG2	liver
11	chr6:25884400-25884600	Enhancers	Pancreas	Pancrea
12	chr6:25884400-25884800	Enhancers	A549	lung
13	chr6:25884400-25885400	Enhancers	Muscle Satellite Cultured Cells	--

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