Variant report

Variant	rs463302
Chromosome Location	chr6:33244716-33244717
allele	C/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	CTCF	chr6:33244683-33245409	K562	blood:	n/a	chr6:33244829-33244842
2	CEBPB	chr6:33244625-33245078	Hela-S3	cervix:	n/a	n/a
3	POLR2A	chr6:33238834-33246727	HepG2	liver:	n/a	n/a
4	ELF1	chr6:33244432-33245625	HCT-116	colon:	n/a	chr6:33244884-33244893 chr6:33244856-33244865 chr6:33244882-33244893 chr6:33244882-33244893
5	POLR2A	chr6:33238829-33246424	HepG2	liver:	n/a	n/a
6	POLR2A	chr6:33241687-33246891	H1-hESC	embryonic stem cell:	n/a	n/a
7	ELK4	chr6:33244565-33245301	HEK293	kidney:	n/a	chr6:33244854-33244865
8	NR3C1	chr6:33244648-33245482	A549	lung:	n/a	chr6:33245041-33245054
9	POLR2A	chr6:33238771-33246916	GM12891	blood:	n/a	n/a
10	TAF1	chr6:33244665-33245377	K562	blood:	n/a	n/a
11	TAF1	chr6:33244638-33245366	K562	blood:	n/a	n/a
12	SIN3AK20	chr6:33244591-33245283	PANC-1	pancreas:	n/a	n/a
13	POLR2A	chr6:33241524-33246131	Hela-S3	cervix:	n/a	n/a
14	MAFF	chr6:33244432-33244843	K562	blood:	n/a	n/a
15	ELK1	chr6:33244398-33245757	K562	blood:	n/a	n/a
16	STAT5A	chr6:33244223-33245577	GM12878	blood:	n/a	chr6:33244913-33244925 chr6:33245039-33245051 chr6:33245045-33245057
17	TEAD4	chr6:33244251-33245345	K562	blood:	n/a	n/a
18	HEY1	chr6:33244177-33245909	HepG2	liver:	n/a	chr6:33244975-33244990
19	STAT3	chr6:33244683-33244803	MCF10A-Er-Src	breast:	n/a	n/a
20	POLR2A	chr6:33243224-33245650	K562	blood:	n/a	n/a
21	YY1	chr6:33244702-33245324	H1-hESC	embryonic stem cell:	n/a	chr6:33245049-33245058 chr6:33244982-33244991
22	REST	chr6:33244693-33244923	GM12878	blood:	n/a	n/a
23	PML	chr6:33244523-33245742	MCF-7	breast:	n/a	n/a
24	GTF2F1	chr6:33244568-33245203	H1-hESC	embryonic stem cell:	n/a	n/a
25	ATF2	chr6:33244225-33245694	H1-hESC	embryonic stem cell:	n/a	n/a
26	SIN3AK20	chr6:33244523-33245083	PFSK-1	brain:	n/a	n/a
27	BCL3	chr6:33244255-33245948	A549	lung:	n/a	chr6:33244666-33244675 chr6:33244856-33244865 chr6:33244978-33244991 chr6:33245005-33245018
28	POLR2A	chr6:33244561-33245518	H1-neurons	neurons:	n/a	n/a
29	SP1	chr6:33244535-33245379	A549	lung:	n/a	chr6:33245048-33245057 chr6:33244921-33244933 chr6:33245048-33245057 chr6:33245047-33245059 chr6:33245048-33245062 chr6:33244912-33244926 chr6:33244923-33244932 chr6:33244922-33244932 chr6:33244921-33244933 chr6:33245049-33245058 chr6:33244922-33244931 chr6:33245047-33245058 chr6:33245047-33245059
30	ELF1	chr6:33244529-33246064	MCF-7	breast:	n/a	chr6:33244884-33244893 chr6:33244856-33244865 chr6:33244882-33244893 chr6:33244882-33244893
31	CHD2	chr6:33244655-33245901	GM12878	blood:	n/a	chr6:33244912-33244922 chr6:33245047-33245057
32	MAX	chr6:33244483-33245429	ECC-1	luminal epithelium:	n/a	n/a
33	TCF12	chr6:33244336-33245951	A549	lung:	n/a	n/a
34	BCL3	chr6:33244384-33245940	A549	lung:	n/a	chr6:33244666-33244675 chr6:33244856-33244865 chr6:33244978-33244991 chr6:33245005-33245018
35	MAX	chr6:33244546-33245177	Hela-S3	cervix:	n/a	n/a
36	POLR2A	chr6:33238743-33246473	GM12892	blood:	n/a	n/a
37	JUND	chr6:33244409-33245727	MCF-7	breast:	n/a	chr6:33245050-33245059
38	MAX	chr6:33244357-33245501	A549	lung:	n/a	n/a
39	ELF1	chr6:33244491-33245761	MCF-7	breast:	n/a	chr6:33244884-33244893 chr6:33244856-33244865 chr6:33244882-33244893 chr6:33244882-33244893
40	ELF1	chr6:33244579-33245638	K562	blood:	n/a	chr6:33244884-33244893 chr6:33244856-33244865 chr6:33244882-33244893 chr6:33244882-33244893
41	POLR2A	chr6:33243512-33246469	GM18505	blood:	n/a	n/a
42	YY1	chr6:33244539-33245391	ECC-1	luminal epithelium:	n/a	chr6:33245049-33245058 chr6:33244982-33244991
43	POLR2A	chr6:33244307-33245354	PBDE	blood:	n/a	n/a
44	JUN	chr6:33244221-33245707	K562	blood:	n/a	chr6:33245050-33245059
45	FOXM1	chr6:33244318-33245470	GM12878	blood:	n/a	n/a
46	PBX3	chr6:33244485-33246141	SK-N-SH	brain:	n/a	n/a
47	GABPA	chr6:33244610-33245054	Hela-S3	cervix:	n/a	n/a
48	POLR2A	chr6:33238799-33249598	PANC-1	pancreas:	n/a	n/a
49	SP4	chr6:33244355-33245397	H1-hESC	embryonic stem cell:	n/a	chr6:33245047-33245063 chr6:33245047-33245058
50	SIN3AK20	chr6:33244408-33245212	A549	lung:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr6:33244709-33244759	GM12892	blood:	n/a
2	chr6:33244709-33244759	ECC-1	luminal epithelium:	n/a
3	chr6:33244715-33244765	IMR90	lung:	fetal
4	chr6:33244709-33244759	IMR90	lung:	fetal
5	chr6:33244709-33244759	Jurkat	blood:	n/a
6	chr6:33244709-33244759	GM06990	blood:	n/a
7	chr6:33244709-33244759	SK-N-MC	brain:	n/a
8	chr6:33244715-33244765	NH-A	brain:	n/a
9	chr6:33244715-33244765	HCPEpiC	choroid plexus:	n/a
10	chr6:33244709-33244759	HPAEpiC	pulmonary alveolar:	n/a
11	chr6:33244715-33244765	CMK	blood:	n/a
12	chr6:33244709-33244759	HepG2	liver:	n/a
13	chr6:33244709-33244759	PFSK-1	brain:	n/a
14	chr6:33244709-33244759	LNCaP	prostate:	n/a
15	chr6:33244709-33244759	HNPCEpiC	eye:	n/a
16	chr6:33244709-33244759	NB4	blood:	n/a
17	chr6:33244715-33244765	PrEC	prostate:	n/a
18	chr6:33244709-33244759	MCF-7	breast:	n/a
19	chr6:33244709-33244759	T-47D	breast:	n/a
20	chr6:33244709-33244759	AG10803	skin:	n/a
21	chr6:33244715-33244765	PANC-1	pancreas:	n/a
22	chr6:33244715-33244765	HCM	heart:	n/a
23	chr6:33244715-33244765	AoSMC	blood vessel:	n/a
24	chr6:33244715-33244765	LNCaP	prostate:	n/a
25	chr6:33244709-33244759	HIPEpiC	eye:	n/a
26	chr6:33244709-33244759	Hepatocyte	liver:	n/a
27	chr6:33244715-33244765	HRE	kidney:	n/a
28	chr6:33244715-33244765	SAEC	small airway:	n/a
29	chr6:33244709-33244759	HCM	heart:	n/a
30	chr6:33244709-33244759	HUVEC	blood vessel:	n/a
31	chr6:33244709-33244759	MCF10A-Er-Src	breast:	n/a
32	chr6:33244715-33244765	HRPEpiC	eye:	n/a
33	chr6:33244709-33244759	PANC-1	pancreas:	n/a
34	chr6:33244709-33244759	AoSMC	blood vessel:	n/a
35	chr6:33244715-33244765	MCF-7	breast:	n/a
36	chr6:33244709-33244759	ovcar-3	ovarian:	n/a
37	chr6:33244715-33244765	GM19239	blood:	n/a
38	chr6:33244709-33244759	A549	lung:	n/a
39	chr6:33244709-33244759	BJ	skin:	n/a
40	chr6:33244709-33244759	HRPEpiC	eye:	n/a
41	chr6:33244709-33244759	AG04450	lung:	fetal
42	chr6:33244715-33244765	HAEpiC	amniotic membrane:	n/a
43	chr6:33244715-33244765	T-47D	breast:	n/a
44	chr6:33244715-33244765	MCF10A-Er-Src	breast:	n/a
45	chr6:33244715-33244765	Hepatocyte	liver:	n/a
46	chr6:33244715-33244765	GM12891	blood:	n/a
47	chr6:33244715-33244765	HIPEpiC	eye:	n/a
48	chr6:33244709-33244759	RPTEC	kidney:	n/a
49	chr6:33244715-33244765	Hela-S3	cervix:	n/a
50	chr6:33244715-33244765	ECC-1	luminal epithelium:	n/a

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	chr6:33243392..33248315-chr6:33357393..33361975,11	K562	blood:
4	chr6:33243299..33244923-chr6:33383429..33386295,2	MCF-7	breast:
5	chr6:33242863..33248981-chr6:33374531..33379553,10	MCF-7	breast:
6	chr6:33237079..33247876-chr6:33369927..33381738,26	K562	blood:
7	chr6:33244541..33246280-chrX:48553569..48556228,2	MCF-7	breast:
8	chr6:32940062..32942357-chr6:33242995..33244738,2	MCF-7	breast:
9	chr6:33244147..33247113-chr6:33398461..33400467,3	K562	blood:
10	chr6:33243260..33246626-chr6:33279357..33283682,8	MCF-7	breast:
11	chr6:33165702..33182742-chr6:33234718..33250379,54	K562	blood:
12	chr6:33237732..33247113-chr6:33390735..33401356,31	K562	blood:
13	chr6:32936829..32939717-chr6:33243245..33245916,3	MCF-7	breast:
14	chr6:32939187..32940741-chr6:33244329..33246573,2	K562	blood:
15	chr6:33237328..33248026-chr6:33370896..33379989,29	K562	blood:
16	chr6:33164650..33184503-chr6:33230350..33245922,64	K562	blood:
17	chr6:33242365..33247657-chr6:33386109..33388284,6	K562	blood:
18	chr6:33244680..33251060-chr6:33375427..33382644,12	MCF-7	breast:
19	chr6:33237283..33247485-chr6:33356185..33362256,17	K562	blood:
20	chr6:33241747..33248128-chr6:33380775..33386072,13	K562	blood:
21	chr6:33242542..33249529-chr6:33381747..33388277,18	K562	blood:
22	chr6:33243431..33246571-chr6:33357252..33359910,3	MCF-7	breast:
23	chr6:33215927..33218801-chr6:33244102..33245865,2	MCF-7	breast:
24	chr17:56708180..56711654-chr6:33242871..33246395,4	MCF-7	breast:
25	chr6:33243334..33245970-chr6:33284249..33287251,3	MCF-7	breast:
26	chr1:28975010..28975525-chr6:33244472..33245436,2	Hela-S3	cervix:

Variant related genes	Relation type
VPS52	TF binding region
B3GALT4	TF binding region
VPS52	CpG island
B3GALT4	CpG island
ENSG00000112473	Chromatin interaction
ENSG00000231925	Chromatin interaction
ENSG00000212195	Chromatin interaction
ENSG00000197283	Chromatin interaction
ENSG00000199036	Chromatin interaction
ENSG00000204231	Chromatin interaction
ENSG00000270103	Chromatin interaction
ENSG00000237649	Chromatin interaction
ENSG00000204227	Chromatin interaction
ENSG00000263756	Chromatin interaction
ENSG00000236104	Chromatin interaction
ENSG00000112514	Chromatin interaction
ENSG00000204256	Chromatin interaction
ENSG00000232940	Chromatin interaction
ENSG00000204257	Chromatin interaction
ENSG00000223837	Chromatin interaction
ENSG00000112511	Chromatin interaction
ENSG00000101945	Chromatin interaction
ENSG00000225463	Chromatin interaction
ENSG00000204228	Chromatin interaction
ENSG00000202441	Chromatin interaction
ENSG00000225644	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs17215210	0.82[AFR][1000 genomes]
rs17221597	0.82[AFR][1000 genomes]
rs17221611	0.82[AFR][1000 genomes]
rs41266713	0.82[AFR][1000 genomes]
rs41266737	0.83[AFR][1000 genomes]
rs460568	0.84[ASN][1000 genomes]
rs465151	0.87[EUR][1000 genomes]
rs72654477	0.83[AFR][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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs463302	B3GALT4	cis	Cerebellum	GTEx

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	chr6:33240200-33244800	Transcr. at gene 5' and 3'	HUES6 Cell Line	embryonic stem cell
5	chr6:33240200-33244800	Transcr. at gene 5' and 3'	iPS-20b Cell Line	embryonic stem cell
6	chr6:33240200-33244800	Transcr. at gene 5' and 3'	A549	lung
7	chr6:33240200-33244800	Transcr. at gene 5' and 3'	K562	blood
8	chr6:33240200-33245800	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr6:33240400-33244800	Transcr. at gene 5' and 3'	Primary T helper cells PMA-I stimulated	--
10	chr6:33240400-33244800	Transcr. at gene 5' and 3'	HSMM	muscle
11	chr6:33240400-33245400	Transcr. at gene 5' and 3'	HMEC	breast
12	chr6:33240400-33246000	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells short term culture	blood
13	chr6:33240400-33246200	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr6:33240600-33244800	Transcr. at gene 5' and 3'	H1 Cell Line	embryonic stem cell
15	chr6:33240600-33244800	Transcr. at gene 5' and 3'	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr6:33240600-33248800	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr6:33241800-33248800	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr6:33242600-33244800	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr6:33243200-33244800	Weak transcription	Ovary	ovary
20	chr6:33243600-33244800	Transcr. at gene 5' and 3'	Fetal Brain Female	brain
21	chr6:33243600-33245000	Strong transcription	HepG2	liver
22	chr6:33243600-33245600	Transcr. at gene 5' and 3'	NHLF	lung
23	chr6:33243800-33244800	Transcr. at gene 5' and 3'	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr6:33244000-33244800	Transcr. at gene 5' and 3'	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr6:33244000-33244800	Flanking Active TSS	Primary T cells from cord blood	blood
26	chr6:33244000-33244800	Enhancers	Placenta Amnion	Placenta Amnion
27	chr6:33244000-33244800	Flanking Active TSS	Rectal Smooth Muscle	rectum
28	chr6:33244000-33244800	Transcr. at gene 5' and 3'	Osteobl	bone
29	chr6:33244200-33244800	Flanking Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr6:33244200-33244800	Transcr. at gene 5' and 3'	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr6:33244200-33244800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
32	chr6:33244200-33244800	Transcr. at gene 5' and 3'	Primary T cells fromperipheralblood	blood
33	chr6:33244200-33244800	Transcr. at gene 5' and 3'	Fetal Adrenal Gland	Adrenal Gland
34	chr6:33244200-33244800	Transcr. at gene 5' and 3'	Fetal Muscle Leg	muscle
35	chr6:33244200-33244800	Transcr. at gene 5' and 3'	Fetal Thymus	thymus
36	chr6:33244200-33244800	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
37	chr6:33244200-33244800	Transcr. at gene 5' and 3'	Skeletal Muscle Male	skeletal muscle
38	chr6:33244200-33245000	Transcr. at gene 5' and 3'	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr6:33244200-33245600	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
40	chr6:33244200-33246200	Active TSS	ES-I3 Cell Line	embryonic stem cell
41	chr6:33244200-33246200	Flanking Active TSS	Primary B cells from cord blood	blood
42	chr6:33244400-33244800	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
43	chr6:33244400-33244800	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
44	chr6:33244400-33244800	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
45	chr6:33244400-33244800	Transcr. at gene 5' and 3'	Primary T killer memory cells from peripheral blood	blood
46	chr6:33244400-33244800	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr6:33244400-33244800	Flanking Active TSS	Adipose Nuclei	Adipose
48	chr6:33244400-33244800	Flanking Active TSS	Brain Hippocampus Middle	brain
49	chr6:33244400-33244800	Flanking Active TSS	Colonic Mucosa	Colon
50	chr6:33244400-33244800	Flanking Active TSS	Fetal Brain Male	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links