Variant report

Variant	rs458434
Chromosome Location	chr6:33242825-33242826
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:79)
CpG islands
(count:0)
Chromatin interactive
region (count:22)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:79 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr6:33241991-33242836	U87	brain:	n/a	n/a
2	POLR2A	chr6:33238834-33246727	HepG2	liver:	n/a	n/a
3	POLR2A	chr6:33242093-33243340	GM12892	blood:	n/a	n/a
4	POLR2A	chr6:33238829-33246424	HepG2	liver:	n/a	n/a
5	POLR2A	chr6:33241687-33246891	H1-hESC	embryonic stem cell:	n/a	n/a
6	PML	chr6:33238698-33243154	GM12878	blood:	n/a	n/a
7	POLR2A	chr6:33238771-33246916	GM12891	blood:	n/a	n/a
8	POLR2A	chr6:33241524-33246131	Hela-S3	cervix:	n/a	n/a
9	POLR2A	chr6:33241531-33243336	GM18951	blood:	n/a	n/a
10	POLR2A	chr6:33238743-33246473	GM12892	blood:	n/a	n/a
11	MXI1	chr6:33238699-33243818	SK-N-SH	brain:	n/a	n/a
12	HEY1	chr6:33241921-33243173	HepG2	liver:	n/a	n/a
13	POLR2A	chr6:33238799-33249598	PANC-1	pancreas:	n/a	n/a
14	POLR2A	chr6:33238786-33246484	HL-60	blood:	n/a	n/a
15	POLR2A	chr6:33238743-33246025	K562	blood:	n/a	n/a
16	POLR2A	chr6:33241881-33243119	ECC-1	luminal epithelium:	n/a	n/a
17	HEY1	chr6:33238730-33245426	K562	blood:	n/a	chr6:33244975-33244990
18	MXI1	chr6:33242217-33243078	K562	blood:	n/a	n/a
19	POLR2A	chr6:33238841-33246850	SK-N-SH	brain:	n/a	n/a
20	POLR2A	chr6:33238813-33246944	GM12878	blood:	n/a	n/a
21	POLR2A	chr6:33241937-33243252	SK-N-SH	brain:	n/a	n/a
22	POLR2A	chr6:33238661-33247019	PFSK-1	brain:	n/a	n/a
23	POLR2A	chr6:33238693-33247581	SK-N-MC	brain:	n/a	n/a
24	POLR2A	chr6:33238873-33246380	K562	blood:	n/a	n/a
25	POLR2A	chr6:33238907-33243453	MCF-7	breast:	n/a	n/a
26	POLR2A	chr6:33238910-33246525	MCF10A-Er-Src	breast:	n/a	n/a
27	POLR2A	chr6:33238801-33246451	GM12892	blood:	n/a	n/a
28	POLR2A	chr6:33241922-33243294	HepG2	liver:	n/a	n/a
29	POLR2A	chr6:33241655-33242963	H1-hESC	embryonic stem cell:	n/a	n/a
30	POLR2A	chr6:33241902-33243222	NB4	blood:	n/a	n/a
31	PML	chr6:33242037-33242918	K562	blood:	n/a	n/a
32	POLR2A	chr6:33238672-33247507	GM12878	blood:	n/a	n/a
33	POLR2A	chr6:33241660-33246396	H1-hESC	embryonic stem cell:	n/a	n/a
34	POLR2A	chr6:33241917-33242830	U87	brain:	n/a	n/a
35	POLR2A	chr6:33238990-33243019	HUVEC	blood vessel:	n/a	n/a
36	POLR2A	chr6:33241914-33243023	HCT-116	colon:	n/a	n/a
37	POLR2A	chr6:33238847-33246460	HUVEC	blood vessel:	n/a	n/a
38	POLR2A	chr6:33241894-33243279	PBDE	blood:	n/a	n/a
39	NFATC1	chr6:33241676-33244103	GM12878	blood:	n/a	n/a
40	POLR2A	chr6:33238740-33248719	HepG2	liver:	n/a	n/a
41	POLR2A	chr6:33242073-33246694	HepG2	liver:	n/a	n/a
42	POLR2A	chr6:33238752-33247553	GM12892	blood:	n/a	n/a
43	POLR2A	chr6:33238876-33243259	HCT-116	colon:	n/a	n/a
44	POLR2A	chr6:33241936-33243106	SK-N-MC	brain:	n/a	n/a
45	POLR2A	chr6:33242121-33243158	GM12878	blood:	n/a	n/a
46	POLR2A	chr6:33242776-33243032	H1-hESC	embryonic stem cell:	n/a	n/a
47	POLR2A	chr6:33242774-33246235	H1-hESC	embryonic stem cell:	n/a	n/a
48	POLR2A	chr6:33241596-33246336	GM12892	blood:	n/a	n/a
49	POLR2A	chr6:33238868-33246449	K562	blood:	n/a	n/a
50	POLR2A	chr6:33238940-33246370	Hela-S3	cervix:	n/a	n/a

No data

(count:22 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:33214775..33224346-chr6:33236521..33248678,40	K562	blood:
2	chr6:33163540..33178083-chr6:33236797..33246926,29	MCF-7	breast:
3	chr6:32935365..32941512-chr6:33237253..33242856,9	MCF-7	breast:
4	chr6:33237079..33247876-chr6:33369927..33381738,26	K562	blood:
5	chr6:33242419..33244049-chr6:33358539..33360870,2	MCF-7	breast:
6	chr12:122883071..122886014-chr6:33242178..33244499,2	K562	blood:
7	chr6:33242345..33244145-chr6:33381102..33383050,3	MCF-7	breast:
8	chr6:33238090..33243099-chr6:33279379..33286881,12	MCF-7	breast:
9	chr6:33168190..33170625-chr6:33239125..33244589,6	MCF-7	breast:
10	chr6:33165702..33182742-chr6:33234718..33250379,54	K562	blood:
11	chr6:33237732..33247113-chr6:33390735..33401356,31	K562	blood:
12	chr6:33237328..33248026-chr6:33370896..33379989,29	K562	blood:
13	chr6:33240213..33242985-chr6:33384063..33385890,2	MCF-7	breast:
14	chr6:33164650..33184503-chr6:33230350..33245922,64	K562	blood:
15	chr6:33242365..33247657-chr6:33386109..33388284,6	K562	blood:
16	chr6:33241732..33243308-chr6:33359602..33361155,2	K562	blood:
17	chr6:33237283..33247485-chr6:33356185..33362256,17	K562	blood:
18	chr6:33241747..33248128-chr6:33380775..33386072,13	K562	blood:
19	chr6:33242542..33249529-chr6:33381747..33388277,18	K562	blood:
20	chr6:33092780..33094332-chr6:33241137..33242898,2	K562	blood:
21	chr6:33160840..33162733-chr6:33241320..33243062,2	K562	blood:
22	chr6:33159618..33162340-chr6:33240515..33243062,2	K562	blood:

No data

Variant related genes	Relation type
VPS52	TF binding region
B3GALT4	TF binding region
RPS18	TF binding region
ENSG00000236104	Chromatin interaction
ENSG00000197283	Chromatin interaction
ENSG00000130779	Chromatin interaction
ENSG00000225463	Chromatin interaction
ENSG00000112514	Chromatin interaction
ENSG00000231925	Chromatin interaction
ENSG00000263756	Chromatin interaction
ENSG00000237649	Chromatin interaction
ENSG00000112473	Chromatin interaction
ENSG00000204231	Chromatin interaction
ENSG00000204227	Chromatin interaction
ENSG00000225644	Chromatin interaction
ENSG00000232940	Chromatin interaction
ENSG00000204228	Chromatin interaction
ENSG00000199036	Chromatin interaction
ENSG00000204256	Chromatin interaction
ENSG00000204248	Chromatin interaction
ENSG00000223837	Chromatin interaction
ENSG00000202441	Chromatin interaction
ENSG00000204257	Chromatin interaction
ENSG00000112511	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs1061801	0.81[ASN][1000 genomes]
rs3445	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs460568	0.88[EUR][1000 genomes]
rs461338	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs462618	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs464921	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs466886	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9277956	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9277958	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9277965	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv462893	chr6:33142539-33256471	Weak transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
2	nsv602830	chr6:33142539-33256471	Enhancers Bivalent Enhancer Flanking Active TSS Genic enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Weak transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
3	nsv830634	chr6:33161217-33330745	Flanking Active TSS Genic enhancers Active TSS Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	139 gene(s)	inside rSNPs	diseases
4	nsv462894	chr6:33174783-33254665	Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	87 gene(s)	inside rSNPs	diseases
5	nsv602831	chr6:33174783-33254665	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	87 gene(s)	inside rSNPs	diseases
6	nsv5249	chr6:33231743-33249478	Strong transcription Weak transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	62 gene(s)	inside rSNPs	diseases
7	nsv830635	chr6:33238005-33413787	Active TSS Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Transcr. at gene 5' and 3' Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	129 gene(s)	inside rSNPs	diseases
8	nsv970109	chr6:33241506-33248502	Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Weak transcription Enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region	36 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs458434	B3GALT4	cis	multi-tissue	Pritchard
rs458434	STK38	cis	parietal	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:33238800-33244800	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
2	chr6:33240000-33244800	Transcr. at gene 5' and 3'	Dnd41	blood
3	chr6:33240000-33245600	Transcr. at gene 5' and 3'	NHEK	skin
4	chr6:33240200-33243400	Transcr. at gene 5' and 3'	Muscle Satellite Cultured Cells	--
5	chr6:33240200-33244800	Transcr. at gene 5' and 3'	HUES6 Cell Line	embryonic stem cell
6	chr6:33240200-33244800	Transcr. at gene 5' and 3'	iPS-20b Cell Line	embryonic stem cell
7	chr6:33240200-33244800	Transcr. at gene 5' and 3'	A549	lung
8	chr6:33240200-33244800	Transcr. at gene 5' and 3'	K562	blood
9	chr6:33240200-33245800	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr6:33240400-33244600	Transcr. at gene 5' and 3'	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr6:33240400-33244600	Transcr. at gene 5' and 3'	HUES64 Cell Line	embryonic stem cell
12	chr6:33240400-33244600	Transcr. at gene 5' and 3'	iPS-18 Cell Line	embryonic stem cell
13	chr6:33240400-33244600	Transcr. at gene 5' and 3'	Breast Myoepithelial Primary Cells	Breast
14	chr6:33240400-33244600	Transcr. at gene 5' and 3'	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr6:33240400-33244600	Transcr. at gene 5' and 3'	Hela-S3	cervix
16	chr6:33240400-33244800	Transcr. at gene 5' and 3'	Primary T helper cells PMA-I stimulated	--
17	chr6:33240400-33244800	Transcr. at gene 5' and 3'	HSMM	muscle
18	chr6:33240400-33245400	Transcr. at gene 5' and 3'	HMEC	breast
19	chr6:33240400-33246000	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells short term culture	blood
20	chr6:33240400-33246200	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr6:33240600-33243000	Transcr. at gene 5' and 3'	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr6:33240600-33243000	Transcr. at gene 5' and 3'	NHLF	lung
23	chr6:33240600-33243200	Transcr. at gene 5' and 3'	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr6:33240600-33243200	Transcr. at gene 5' and 3'	NH-A	brain
25	chr6:33240600-33244200	Genic enhancers	Primary B cells from peripheral blood	blood
26	chr6:33240600-33244600	Transcr. at gene 5' and 3'	HUES48 Cell Line	embryonic stem cell
27	chr6:33240600-33244600	Transcr. at gene 5' and 3'	iPS-15b Cell Line	embryonic stem cell
28	chr6:33240600-33244800	Transcr. at gene 5' and 3'	H1 Cell Line	embryonic stem cell
29	chr6:33240600-33244800	Transcr. at gene 5' and 3'	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr6:33240600-33248800	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr6:33240800-33243000	Transcr. at gene 5' and 3'	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr6:33240800-33243000	Transcr. at gene 5' and 3'	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr6:33240800-33243000	Transcr. at gene 5' and 3'	HepG2	liver
34	chr6:33240800-33244200	Genic enhancers	Primary T cells fromperipheralblood	blood
35	chr6:33240800-33244400	Genic enhancers	Primary T helper cells fromperipheralblood	blood
36	chr6:33240800-33244400	Genic enhancers	Placenta	Placenta
37	chr6:33241000-33244400	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
38	chr6:33241200-33243200	Transcr. at gene 5' and 3'	Psoas Muscle	Psoas
39	chr6:33241200-33243800	Transcr. at gene 5' and 3'	HUVEC	blood vessel
40	chr6:33241200-33244200	Genic enhancers	Cortex derived primary cultured neurospheres	brain
41	chr6:33241200-33244200	Genic enhancers	Fetal Heart	heart
42	chr6:33241200-33244200	Genic enhancers	Fetal Thymus	thymus
43	chr6:33241200-33244200	Genic enhancers	Skeletal Muscle Male	skeletal muscle
44	chr6:33241200-33244400	Genic enhancers	Primary monocytes fromperipheralblood	blood
45	chr6:33241200-33244400	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
46	chr6:33241200-33244400	Genic enhancers	Adipose Nuclei	Adipose
47	chr6:33241200-33244400	Genic enhancers	Liver	Liver
48	chr6:33241200-33244600	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr6:33241400-33243400	Genic enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
50	chr6:33241400-33243800	Genic enhancers	Rectal Mucosa Donor 31	rectum

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