Variant report

Variant	rs1611285
Chromosome Location	chr6:29731787-29731788
allele	C/T
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	FOS	chr6:29731200-29731900	HUVEC	blood vessel:	n/a	chr6:29731638-29731650 chr6:29731608-29731619
2	TCF12	chr6:29731113-29731957	SK-N-SH	brain:	n/a	n/a
3	JUN	chr6:29731353-29731895	HUVEC	blood vessel:	n/a	chr6:29731638-29731650
4	PBX3	chr6:29731251-29731812	SK-N-SH	brain:	n/a	n/a
5	POLR2A	chr6:29731297-29731849	HUVEC	blood vessel:	n/a	n/a
6	FOS	chr6:29731419-29731859	MCF10A-Er-Src	breast:	n/a	chr6:29731638-29731650 chr6:29731608-29731619
7	TCF12	chr6:29731126-29732002	SK-N-SH	brain:	n/a	n/a
8	REST	chr6:29731232-29731897	PFSK-1	brain:	n/a	chr6:29731279-29731289
9	STAT3	chr6:29731409-29731815	MCF10A-Er-Src	breast:	n/a	n/a
10	EP300	chr6:29731435-29731788	Hela-S3	cervix:	n/a	n/a
11	NFIC	chr6:29731207-29731793	SK-N-SH	brain:	n/a	n/a
12	MYC	chr6:29731415-29731882	MCF10A-Er-Src	breast:	n/a	n/a
13	FOS	chr6:29731418-29731842	MCF10A-Er-Src	breast:	n/a	chr6:29731638-29731650 chr6:29731608-29731619
14	FOS	chr6:29731366-29732011	MCF10A-Er-Src	breast:	n/a	chr6:29731638-29731650 chr6:29731608-29731619
15	POLR2A	chr6:29730447-29731941	PFSK-1	brain:	n/a	n/a
16	TAF1	chr6:29731271-29731809	PFSK-1	brain:	n/a	n/a
17	POLR2A	chr6:29731314-29731829	HUVEC	blood vessel:	n/a	n/a
18	CEBPB	chr6:29731363-29731796	Hela-S3	cervix:	n/a	n/a
19	FOS	chr6:29731355-29732022	MCF10A-Er-Src	breast:	n/a	chr6:29731638-29731650 chr6:29731608-29731619
20	NFIC	chr6:29731358-29731791	SK-N-SH	brain:	n/a	n/a
21	POLR2A	chr6:29730213-29732222	PFSK-1	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:29719431..29722230-chr6:29728984..29731849,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000270896	TF binding region
ENSG00000272236	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs1611283	0.81[ASN][1000 genomes]
rs2508050	0.89[ASN][1000 genomes]
rs2517933	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2517934	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2517938	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2517941	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2517943	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2523385	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2523390	0.85[AFR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2523401	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2523407	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2743950	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2844833	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2844845	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs422343	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs730858	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9258255	0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9258256	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9258278	1.00[ASN][1000 genomes]
rs9258285	0.84[ASN][1000 genomes]
rs9258294	1.00[ASN][1000 genomes]
rs9258305	1.00[ASN][1000 genomes]
rs9258373	0.96[ASN][1000 genomes]
rs9258384	1.00[ASN][1000 genomes]
rs9258393	1.00[ASN][1000 genomes]
rs9258434	0.89[ASN][1000 genomes]
rs9258441	0.93[ASN][1000 genomes]
rs9258451	0.82[ASN][1000 genomes]
rs9258508	0.89[ASN][1000 genomes]
rs9258525	0.89[ASN][1000 genomes]
rs9258605	0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv20940	chr6:29653954-29923410	Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
2	nsv428475	chr6:29659525-29763392	Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
3	nsv428139	chr6:29659525-29892317	Bivalent Enhancer Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
4	nsv427749	chr6:29659525-29975144	Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
5	nsv508397	chr6:29663132-29761448	Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription Transcr. at gene 5' and 3' Enhancers Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
6	esv1794141	chr6:29670915-29765814	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
7	nsv10809	chr6:29692573-29794119	Flanking Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
8	nsv883532	chr6:29703262-29814963	Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Weak transcription Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
9	esv3441842	chr6:29715749-29942950	Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers Bivalent Enhancer Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
10	nsv883535	chr6:29725321-29741338	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
11	esv11180	chr6:29729381-29800066	Enhancers Bivalent Enhancer Weak transcription Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1611285	HIST1H2BE	cis	parietal	SCAN
rs1611285	BTN3A1	cis	parietal	SCAN

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:29728600-29737200	Weak transcription	Lung	lung
2	chr6:29729000-29733800	Enhancers	HMEC	breast
3	chr6:29729400-29733400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr6:29729600-29733200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr6:29729600-29733400	Enhancers	NHEK	skin
6	chr6:29729600-29733600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr6:29729600-29733600	Enhancers	Esophagus	oesophagus
8	chr6:29729800-29733800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr6:29730000-29732000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr6:29730200-29731800	Enhancers	Adipose Nuclei	Adipose
11	chr6:29730200-29733000	Enhancers	HUVEC	blood vessel
12	chr6:29730200-29733400	Enhancers	NHDF-Ad	bronchial
13	chr6:29730200-29734600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr6:29730400-29732600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr6:29730400-29732800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr6:29730400-29733200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr6:29730600-29731800	Enhancers	Fetal Lung	lung
18	chr6:29730600-29732600	Enhancers	GM12878-XiMat	blood
19	chr6:29730600-29733400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr6:29730600-29733400	Enhancers	Muscle Satellite Cultured Cells	--
21	chr6:29731000-29733400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr6:29731200-29731800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr6:29731200-29733400	Enhancers	Osteobl	bone
24	chr6:29731400-29731800	Enhancers	Monocytes-CD14+_RO01746	blood
25	chr6:29731400-29739000	Weak transcription	Spleen	Spleen
26	chr6:29731600-29732000	Enhancers	Stomach Smooth Muscle	stomach
27	chr6:29731600-29732400	Enhancers	Placenta Amnion	Placenta Amnion
28	chr6:29731600-29732800	Enhancers	NHLF	lung
29	chr6:29731600-29733400	Enhancers	Hela-S3	cervix
30	chr6:29731600-29738800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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