Variant report

Variant	rs464921
Chromosome Location	chr6:33240506-33240507
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:123)
CpG islands
(count:122)
Chromatin interactive
region (count:36)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:123 , 50 per page) page: 1 2 3

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr6:33238834-33246727	HepG2	liver:	n/a	n/a
2	POLR2A	chr6:33238760-33241532	GM12891	blood:	n/a	n/a
3	POLR2A	chr6:33238829-33246424	HepG2	liver:	n/a	n/a
4	PML	chr6:33238698-33243154	GM12878	blood:	n/a	n/a
5	POLR2A	chr6:33238876-33241752	HepG2	liver:	n/a	n/a
6	MAX	chr6:33239133-33240515	MCF-7	breast:	n/a	n/a
7	POLR2A	chr6:33238771-33246916	GM12891	blood:	n/a	n/a
8	CEBPD	chr6:33239015-33240685	K562	blood:	n/a	n/a
9	MXI1	chr6:33238746-33241055	IMR90	lung:	n/a	n/a
10	POLR2A	chr6:33238903-33241409	GM12891	blood:	n/a	n/a
11	POLR2A	chr6:33239090-33241526	ECC-1	luminal epithelium:	n/a	n/a
12	POLR2A	chr6:33238864-33240991	HCT-116	colon:	n/a	n/a
13	POLR2A	chr6:33238743-33246473	GM12892	blood:	n/a	n/a
14	TBL1XR1	chr6:33238847-33241192	K562	blood:	n/a	n/a
15	TEAD4	chr6:33238694-33241455	K562	blood:	n/a	n/a
16	MYC	chr6:33238842-33240651	K562	blood:	n/a	n/a
17	MXI1	chr6:33238699-33243818	SK-N-SH	brain:	n/a	n/a
18	POLR2A	chr6:33238799-33249598	PANC-1	pancreas:	n/a	n/a
19	TBP	chr6:33238928-33240936	Hela-S3	cervix:	n/a	n/a
20	POLR2A	chr6:33238951-33240564	H1-hESC	embryonic stem cell:	n/a	n/a
21	PML	chr6:33238711-33241787	K562	blood:	n/a	n/a
22	EP300	chr6:33240218-33240627	T-47D	breast:	n/a	n/a
23	POLR2A	chr6:33238786-33246484	HL-60	blood:	n/a	n/a
24	KAP1	chr6:33238894-33241036	K562	blood:	n/a	n/a
25	POLR2A	chr6:33238743-33246025	K562	blood:	n/a	n/a
26	HEY1	chr6:33238730-33245426	K562	blood:	n/a	chr6:33244975-33244990
27	REST	chr6:33238669-33240570	H1-neurons	neurons:	n/a	n/a
28	PML	chr6:33238747-33240578	K562	blood:	n/a	n/a
29	POLR2A	chr6:33238841-33246850	SK-N-SH	brain:	n/a	n/a
30	CEBPB	chr6:33240366-33241462	GM12878	blood:	n/a	chr6:33240666-33240678
31	POLR2A	chr6:33238919-33241460	K562	blood:	n/a	n/a
32	POLR2A	chr6:33238813-33246944	GM12878	blood:	n/a	n/a
33	POLR2A	chr6:33239173-33241412	HepG2	liver:	n/a	n/a
34	POLR2A	chr6:33238661-33247019	PFSK-1	brain:	n/a	n/a
35	POLR2A	chr6:33238693-33247581	SK-N-MC	brain:	n/a	n/a
36	POLR2A	chr6:33239093-33241037	H1-hESC	embryonic stem cell:	n/a	n/a
37	POLR2A	chr6:33239106-33241447	U87	brain:	n/a	n/a
38	TRIM28	chr6:33238750-33240558	K562	blood:	n/a	n/a
39	POLR2A	chr6:33238895-33241487	K562	blood:	n/a	n/a
40	TAF1	chr6:33238790-33240541	ECC-1	luminal epithelium:	n/a	n/a
41	MTA3	chr6:33238814-33240595	GM12878	blood:	n/a	n/a
42	POLR2A	chr6:33238873-33246380	K562	blood:	n/a	n/a
43	MYC	chr6:33238876-33240926	K562	blood:	n/a	n/a
44	ELK1	chr6:33238879-33240625	K562	blood:	n/a	n/a
45	POLR2A	chr6:33238907-33243453	MCF-7	breast:	n/a	n/a
46	POLR2A	chr6:33238910-33246525	MCF10A-Er-Src	breast:	n/a	n/a
47	POLR2A	chr6:33238801-33246451	GM12892	blood:	n/a	n/a
48	STAT5A	chr6:33238840-33241038	K562	blood:	n/a	chr6:33240627-33240638
49	POLR2A	chr6:33238892-33240946	Raji	blood:	n/a	n/a
50	MYC	chr6:33239146-33240849	K562	blood:	n/a	n/a

(count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr6:33240471-33240521	IMR90	lung:	fetal
2	chr6:33240468-33240518	ECC-1	luminal epithelium:	n/a
3	chr6:33240468-33240518	RPTEC	kidney:	n/a
4	chr6:33240468-33240518	T-47D	breast:	n/a
5	chr6:33240471-33240521	SK-N-MC	brain:	n/a
6	chr6:33240471-33240521	GM12878	blood:	n/a
7	chr6:33240468-33240518	AG10803	skin:	n/a
8	chr6:33240471-33240521	MCF10A-Er-Src	breast:	n/a
9	chr6:33240471-33240521	Hela-S3	cervix:	n/a
10	chr6:33240468-33240518	AG09309	skin:	n/a
11	chr6:33240471-33240521	GM12891	blood:	n/a
12	chr6:33240471-33240521	HIPEpiC	eye:	n/a
13	chr6:33240468-33240518	SK-N-SH	brain:	n/a
14	chr6:33240471-33240521	U87	brain:	n/a
15	chr6:33240468-33240518	Hepatocyte	liver:	n/a
16	chr6:33240468-33240518	GM19239	blood:	n/a
17	chr6:33240471-33240521	Caco-2	colon:	n/a
18	chr6:33240471-33240521	HEK293	kidney:	embryo
19	chr6:33240471-33240521	K562	blood:	n/a
20	chr6:33240471-33240521	SKMC	muscle:	n/a
21	chr6:33240471-33240521	SK-N-SH	brain:	n/a
22	chr6:33240471-33240521	H1-hESC	embryonic stem cell:	embryo
23	chr6:33240471-33240521	HCF	heart:	n/a
24	chr6:33240468-33240518	HEK293	kidney:	embryo
25	chr6:33240468-33240518	GM06990	blood:	n/a
26	chr6:33240471-33240521	GM19239	blood:	n/a
27	chr6:33240468-33240518	HCF	heart:	n/a
28	chr6:33240471-33240521	AG10803	skin:	n/a
29	chr6:33240468-33240518	HPAEpiC	pulmonary alveolar:	n/a
30	chr6:33240468-33240518	HCPEpiC	choroid plexus:	n/a
31	chr6:33240471-33240521	HCPEpiC	choroid plexus:	n/a
32	chr6:33240471-33240521	GM06990	blood:	n/a
33	chr6:33240471-33240521	T-47D	breast:	n/a
34	chr6:33240468-33240518	HRE	kidney:	n/a
35	chr6:33240468-33240518	HepG2	liver:	n/a
36	chr6:33240468-33240518	BJ	skin:	n/a
37	chr6:33240471-33240521	HCM	heart:	n/a
38	chr6:33240471-33240521	PFSK-1	brain:	n/a
39	chr6:33240468-33240518	AoSMC	blood vessel:	n/a
40	chr6:33240468-33240518	PrEC	prostate:	n/a
41	chr6:33240471-33240521	HRPEpiC	eye:	n/a
42	chr6:33240471-33240521	AG09309	skin:	n/a
43	chr6:33240471-33240521	HRCEpiC	kidney:	n/a
44	chr6:33240471-33240521	CMK	blood:	n/a
45	chr6:33240468-33240518	H1-hESC	embryonic stem cell:	embryo
46	chr6:33240471-33240521	ECC-1	luminal epithelium:	n/a
47	chr6:33240471-33240521	RPTEC	kidney:	n/a
48	chr6:33240468-33240518	SK-N-MC	brain:	n/a
49	chr6:33240468-33240518	GM12891	blood:	n/a
50	chr6:33240468-33240518	AG09319	gingival:	n/a

(count:36 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:33215556..33218937-chr6:33237888..33241355,8	MCF-7	breast:
2	chr6:33214775..33224346-chr6:33236521..33248678,40	K562	blood:
3	chr6:33163540..33178083-chr6:33236797..33246926,29	MCF-7	breast:
4	chr6:33239039..33242495-chr6:33357243..33362134,5	MCF-7	breast:
5	chr6:32935365..32941512-chr6:33237253..33242856,9	MCF-7	breast:
6	chr6:33237079..33247876-chr6:33369927..33381738,26	K562	blood:
7	chr6:33240007..33241601-chr6:33553728..33555294,2	K562	blood:
8	chr6:32942493..32944074-chr6:33239373..33240940,2	K562	blood:
9	chr6:33239756..33241300-chr6:42712858..42715263,2	MCF-7	breast:
10	chr6:33171159..33172807-chr6:33239561..33241466,2	MCF-7	breast:
11	chr6:33238090..33243099-chr6:33279379..33286881,12	MCF-7	breast:
12	chr6:33239271..33241277-chr6:33383669..33386403,3	MCF-7	breast:
13	chr6:33168190..33170625-chr6:33239125..33244589,6	MCF-7	breast:
14	chr6:32942574..32944407-chr6:33239254..33240873,2	K562	blood:
15	chr6:33165702..33182742-chr6:33234718..33250379,54	K562	blood:
16	chr6:33237732..33247113-chr6:33390735..33401356,31	K562	blood:
17	chr6:33238428..33241280-chr6:33357854..33362793,6	MCF-7	breast:
18	chr6:33237157..33241221-chr6:33375922..33380109,6	MCF-7	breast:
19	chr6:33237639..33241732-chr6:33383253..33390116,11	K562	blood:
20	chr6:33215322..33223570-chr6:33237379..33242085,16	MCF-7	breast:
21	chr6:33237328..33248026-chr6:33370896..33379989,29	K562	blood:
22	chr6:33238401..33240913-chr6:33381042..33383923,3	MCF-7	breast:
23	chr6:33240213..33242985-chr6:33384063..33385890,2	MCF-7	breast:
24	chr6:33164650..33184503-chr6:33230350..33245922,64	K562	blood:
25	chr6:33239712..33240527-chr9:117349738..117350731,2	Hela-S3	cervix:
26	chr6:32934872..32941448-chr6:33236243..33241295,9	MCF-7	breast:
27	chr6:33237283..33247485-chr6:33356185..33362256,17	K562	blood:
28	chr6:32935501..32940970-chr6:33237778..33241596,10	K562	blood:
29	chr6:32819661..32822280-chr6:33238410..33240981,2	MCF-7	breast:
30	chr21:46236119..46237973-chr6:33239831..33242378,2	K562	blood:
31	chr6:33173334..33178624-chr6:33237900..33241664,7	MCF-7	breast:
32	chr6:33237283..33241357-chr6:33358017..33360541,6	K562	blood:
33	chr6:33237802..33241730-chr6:33382199..33389112,10	K562	blood:
34	chr6:32920379..32922659-chr6:33240003..33242483,2	MCF-7	breast:
35	chr6:32933888..32938246-chr6:33239158..33241596,4	K562	blood:
36	chr13:91999607..92001112-chr6:33239163..33241434,2	K562	blood:

No data

Variant related genes	Relation type
B3GALT4	TF binding region
VPS52	TF binding region
RPS18	TF binding region
VPS52	CpG island
RPS18	CpG island
B3GALT4	CpG island
ENSG00000240065	Chromatin interaction
ENSG00000225463	Chromatin interaction
ENSG00000184900	Chromatin interaction
ENSG00000112473	Chromatin interaction
ENSG00000204228	Chromatin interaction
ENSG00000199036	Chromatin interaction
ENSG00000204256	Chromatin interaction
ENSG00000204231	Chromatin interaction
ENSG00000197283	Chromatin interaction
ENSG00000237649	Chromatin interaction
ENSG00000124659	Chromatin interaction
ENSG00000112511	Chromatin interaction
ENSG00000112514	Chromatin interaction
ENSG00000215417	Chromatin interaction
ENSG00000204227	Chromatin interaction
ENSG00000223837	Chromatin interaction
ENSG00000232940	Chromatin interaction
ENSG00000202441	Chromatin interaction
ENSG00000236104	Chromatin interaction
ENSG00000263756	Chromatin interaction
ENSG00000168394	Chromatin interaction
ENSG00000204257	Chromatin interaction
ENSG00000225644	Chromatin interaction
ENSG00000231925	Chromatin interaction
ENSG00000136888	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs3445	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs458434	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs460568	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs461338	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs462618	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs466886	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9277956	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9277958	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9277965	0.87[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	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs464921	STK38	cis	parietal	SCAN
rs464921	B3GALT4	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:33238200-33240600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr6:33238600-33241800	Active TSS	GM12878-XiMat	blood
3	chr6:33238800-33240600	Active TSS	H1 Cell Line	embryonic stem cell
4	chr6:33238800-33240600	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr6:33238800-33240600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr6:33238800-33240600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr6:33238800-33240600	Active TSS	HUES48 Cell Line	embryonic stem cell
8	chr6:33238800-33240600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr6:33238800-33240600	Active TSS	Fetal Muscle Trunk	muscle
10	chr6:33238800-33240600	Active TSS	Left Ventricle	heart
11	chr6:33238800-33240600	Active TSS	Psoas Muscle	Psoas
12	chr6:33238800-33240600	Active TSS	NHLF	lung
13	chr6:33238800-33240800	Active TSS	Ovary	ovary
14	chr6:33238800-33241200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr6:33238800-33241200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr6:33238800-33241200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
17	chr6:33238800-33241200	Active TSS	Lung	lung
18	chr6:33238800-33241200	Active TSS	Pancreas	Pancrea
19	chr6:33238800-33241200	Active TSS	Sigmoid Colon	Sigmoid Colon
20	chr6:33238800-33241400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
21	chr6:33238800-33241400	Active TSS	Right Atrium	heart
22	chr6:33238800-33241800	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr6:33238800-33244800	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
24	chr6:33239000-33240600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr6:33239000-33240600	Active TSS	iPS-15b Cell Line	embryonic stem cell
26	chr6:33239000-33240600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr6:33239000-33240600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr6:33239000-33240600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr6:33239000-33240600	Active TSS	Fetal Intestine Large	intestine
30	chr6:33239000-33240600	Active TSS	Fetal Intestine Small	intestine
31	chr6:33239000-33240600	Bivalent/Poised TSS	HepG2	liver
32	chr6:33239000-33240600	Active TSS	NH-A	brain
33	chr6:33239000-33240800	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr6:33239000-33241000	Active TSS	HSMMtube	muscle
35	chr6:33239000-33241200	Active TSS	Esophagus	oesophagus
36	chr6:33239200-33240600	Active TSS	Colonic Mucosa	Colon
37	chr6:33239200-33240800	Active TSS	Right Ventricle	heart
38	chr6:33239200-33241200	Active TSS	Pancreatic Islets	Pancreatic Islet
39	chr6:33239800-33240600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
40	chr6:33239800-33240600	Flanking Active TSS	Primary B cells from cord blood	blood
41	chr6:33239800-33240800	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
42	chr6:33240000-33240600	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
43	chr6:33240000-33240600	Flanking Active TSS	Primary B cells from peripheral blood	blood
44	chr6:33240000-33240600	Flanking Active TSS	Primary T cells fromperipheralblood	blood
45	chr6:33240000-33240600	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
46	chr6:33240000-33240600	Flanking Active TSS	Fetal Thymus	thymus
47	chr6:33240000-33240600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
48	chr6:33240000-33240800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
49	chr6:33240000-33240800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
50	chr6:33240000-33240800	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin

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