Variant report

Variant	rs756139
Chromosome Location	chr6:33755541-33755542
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:40)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:40 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr6:33754660-33756447	PFSK-1	brain:	n/a	n/a
2	MAZ	chr6:33754791-33757409	IMR90	lung:	n/a	chr6:33756978-33756987
3	POLR2A	chr6:33755036-33756338	PANC-1	pancreas:	n/a	n/a
4	CHD1	chr6:33753489-33757327	IMR90	lung:	n/a	n/a
5	POLR2A	chr6:33754637-33757242	SK-N-MC	brain:	n/a	n/a
6	POLR2A	chr6:33755375-33757546	GM12878	blood:	n/a	n/a
7	POLR2A	chr6:33754307-33756475	PANC-1	pancreas:	n/a	n/a
8	POLR2A	chr6:33755402-33757555	GM12892	blood:	n/a	n/a
9	FOXA1	chr6:33755468-33755729	T-47D	breast:	n/a	n/a
10	FOXA1	chr6:33755490-33756178	HepG2	liver:	n/a	n/a
11	POLR2A	chr6:33754123-33757999	HUVEC	blood vessel:	n/a	n/a
12	GATA2	chr6:33755336-33756232	HUVEC	blood vessel:	n/a	chr6:33755580-33755593 chr6:33755582-33755591
13	POLR2A	chr6:33754585-33758231	HepG2	liver:	n/a	n/a
14	POLR2A	chr6:33755392-33757228	K562	blood:	n/a	n/a
15	POLR2A	chr6:33755421-33757205	H1-hESC	embryonic stem cell:	n/a	n/a
16	RCOR1	chr6:33755463-33756254	K562	blood:	n/a	n/a
17	MXI1	chr6:33754826-33757645	IMR90	lung:	n/a	n/a
18	POLR2A	chr6:33754388-33756268	K562	blood:	n/a	n/a
19	HCFC1	chr6:33754888-33757740	Hela-S3	cervix:	n/a	n/a
20	MYC	chr6:33755432-33756293	K562	blood:	n/a	n/a
21	POLR2A	chr6:33755121-33756356	GM12878	blood:	n/a	n/a
22	POLR2A	chr6:33754812-33757308	HUVEC	blood vessel:	n/a	n/a
23	HDAC2	chr6:33755473-33755979	K562	blood:	n/a	n/a
24	MXI1	chr6:33755276-33757747	SK-N-SH	brain:	n/a	n/a
25	POLR2A	chr6:33754909-33758028	IMR90	lung:	n/a	n/a
26	TEAD4	chr6:33755361-33756315	K562	blood:	n/a	n/a
27	SPI1	chr6:33755501-33756188	GM12878	blood:	n/a	chr6:33755847-33755854
28	MTA3	chr6:33755260-33757493	GM12878	blood:	n/a	n/a
29	POLR2A	chr6:33754751-33757465	HUVEC	blood vessel:	n/a	n/a
30	KAP1	chr6:33755459-33756059	HEK293	kidney:	n/a	n/a
31	POLR2A	chr6:33754863-33757424	HUVEC	blood vessel:	n/a	n/a
32	HDAC2	chr6:33755413-33755886	K562	blood:	n/a	n/a
33	MAX	chr6:33755439-33757185	K562	blood:	n/a	chr6:33756978-33756987
34	PML	chr6:33755430-33756360	GM12878	blood:	n/a	n/a
35	FOS	chr6:33755132-33756163	HUVEC	blood vessel:	n/a	chr6:33755473-33755482
36	POLR2A	chr6:33755539-33757140	ECC-1	luminal epithelium:	n/a	n/a
37	NR2F2	chr6:33755349-33756371	K562	blood:	n/a	n/a
38	POLR2A	chr6:33754903-33758533	HUVEC	blood vessel:	n/a	n/a
39	POLR2A	chr6:33755474-33756305	GM12891	blood:	n/a	n/a
40	POLR2A	chr6:33755024-33757428	MCF10A-Er-Src	breast:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:33677680..33679812-chr6:33755384..33758328,2	MCF-7	breast:
2	chr6:33677771..33685795-chr6:33753004..33758704,10	MCF-7	breast:
3	chr6:33755468..33757115-chr6:34205033..34207556,2	MCF-7	breast:
4	chr6:33754851..33757425-chr6:33862551..33864997,3	MCF-7	breast:
5	chr6:33743352..33745913-chr6:33755354..33756938,3	MCF-7	breast:
6	chr6:33678014..33680671-chr6:33755515..33757218,2	K562	blood:
7	chr6:33550386..33552584-chr6:33755194..33756833,2	MCF-7	breast:

No data

Variant related genes	Relation type
LEMD2	TF binding region
ENSG00000161904	Chromatin interaction
ENSG00000137288	Chromatin interaction
ENSG00000249346	Chromatin interaction
ENSG00000137309	Chromatin interaction
ENSG00000204188	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10755683	0.95[AFR][1000 genomes];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10947436	0.85[ASW][hapmap];0.85[TSI][hapmap];0.96[YRI][hapmap];0.88[EUR][1000 genomes]
rs11751943	0.87[EUR][1000 genomes]
rs1318691	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1536500	0.82[EUR][1000 genomes]
rs1536501	0.92[ASW][hapmap];0.92[YRI][hapmap];0.85[EUR][1000 genomes]
rs1547668	0.81[YRI][hapmap]
rs1998949	0.82[EUR][1000 genomes]
rs2182658	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.99[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2182659	0.85[ASW][hapmap];0.85[TSI][hapmap];0.96[YRI][hapmap];0.88[EUR][1000 genomes]
rs2395399	1.00[CHB][hapmap];0.83[ASN][1000 genomes]
rs2395401	0.85[ASW][hapmap];0.80[MKK][hapmap];0.85[TSI][hapmap];0.96[YRI][hapmap];0.81[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs2395446	0.80[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2395447	0.88[EUR][1000 genomes]
rs4711350	0.85[TSI][hapmap];0.88[EUR][1000 genomes]
rs4713676	0.87[EUR][1000 genomes]
rs4713685	1.00[CHB][hapmap];0.83[ASN][1000 genomes]
rs4996879	0.83[EUR][1000 genomes]
rs530614	0.92[ASW][hapmap];0.92[YRI][hapmap]
rs545787	1.00[JPT][hapmap]
rs568901	0.82[JPT][hapmap]
rs602399	0.92[ASW][hapmap];0.92[YRI][hapmap]
rs652049	0.92[ASW][hapmap];0.92[YRI][hapmap]
rs6921772	0.99[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7449707	0.86[EUR][1000 genomes]
rs751727	0.81[YRI][hapmap];0.88[EUR][1000 genomes]
rs756138	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7739273	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7752348	0.81[CEU][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9380379	0.91[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.94[TSI][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs943464	0.81[YRI][hapmap];0.85[EUR][1000 genomes]
rs943465	1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs943472	0.85[ASW][hapmap];0.85[TSI][hapmap];0.96[YRI][hapmap];0.87[EUR][1000 genomes]
rs943473	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs943476	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9461905	0.82[EUR][1000 genomes]
rs9461907	0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv885772	chr6:33638180-33767727	Bivalent Enhancer Genic enhancers Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	28 gene(s)	inside rSNPs	diseases
2	nsv462897	chr6:33717770-33778964	Genic enhancers Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv602839	chr6:33717770-33778964	Enhancers Genic enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv462898	chr6:33723383-33768897	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
5	nsv602840	chr6:33723383-33768897	Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
6	esv3436027	chr6:33754374-33758772	Active TSS Enhancers Genic enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs756139	BAK1	cis	lymphoblastoid	seeQTL
rs756139	LEMD2	cis	cerebellum	SCAN
rs756139	C6orf125	cis	parietal	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:33752600-33755600	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
2	chr6:33753000-33756000	Flanking Active TSS	HUVEC	blood vessel
3	chr6:33753200-33755600	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
4	chr6:33753400-33755600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr6:33753400-33755800	Enhancers	Spleen	Spleen
6	chr6:33753800-33755600	Enhancers	Small Intestine	intestine
7	chr6:33753800-33755800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr6:33754000-33755800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr6:33754000-33756000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr6:33754200-33756400	Transcr. at gene 5' and 3'	Dnd41	blood
11	chr6:33754400-33755600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr6:33754400-33755800	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
13	chr6:33754400-33755800	Enhancers	Placenta Amnion	Placenta Amnion
14	chr6:33754400-33756000	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
15	chr6:33754400-33756000	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
16	chr6:33754400-33756200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr6:33754400-33756200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr6:33754600-33755600	Enhancers	Aorta	Aorta
19	chr6:33754600-33755800	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
20	chr6:33754600-33755800	Flanking Active TSS	GM12878-XiMat	blood
21	chr6:33754600-33755800	Flanking Active TSS	NHDF-Ad	bronchial
22	chr6:33754600-33756000	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
23	chr6:33754600-33756000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr6:33754600-33756000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
25	chr6:33754600-33756000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
26	chr6:33754600-33756000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr6:33754800-33755600	Flanking Active TSS	Pancreatic Islets	Pancreatic Islet
28	chr6:33754800-33755600	Transcr. at gene 5' and 3'	Fetal Lung	lung
29	chr6:33754800-33755600	Enhancers	Sigmoid Colon	Sigmoid Colon
30	chr6:33754800-33755600	Transcr. at gene 5' and 3'	Stomach Smooth Muscle	stomach
31	chr6:33754800-33755800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
32	chr6:33754800-33755800	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
33	chr6:33754800-33755800	Flanking Active TSS	NH-A	brain
34	chr6:33754800-33756000	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
35	chr6:33754800-33756000	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
36	chr6:33754800-33756000	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr6:33754800-33756000	Flanking Active TSS	Brain Anterior Caudate	brain
38	chr6:33754800-33756000	Flanking Active TSS	Hela-S3	cervix
39	chr6:33754800-33756000	Flanking Active TSS	NHLF	lung
40	chr6:33754800-33756200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr6:33754800-33756200	Flanking Active TSS	Adipose Nuclei	Adipose
42	chr6:33755000-33755600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr6:33755000-33755600	Enhancers	Primary monocytes fromperipheralblood	blood
44	chr6:33755000-33755600	Enhancers	Gastric	stomach
45	chr6:33755000-33755800	Transcr. at gene 5' and 3'	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr6:33755000-33755800	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
47	chr6:33755000-33755800	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
48	chr6:33755000-33755800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr6:33755000-33755800	Flanking Active TSS	Duodenum Mucosa	Duodenum
50	chr6:33755000-33755800	Flanking Active TSS	Rectal Mucosa Donor 29	rectum

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