Variant report

Variant	rs4760653
Chromosome Location	chr12:48175791-48175792
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:59)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:59 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr12:48174429-48176133	PFSK-1	brain:	n/a	n/a
2	POLR2A	chr12:48174640-48177283	K562	blood:	n/a	n/a
3	ZNF263	chr12:48175444-48176043	HEK293-T-REx	kidney:	n/a	n/a
4	GATA3	chr12:48175593-48176112	T-47D	breast:	n/a	n/a
5	POLR2A	chr12:48174533-48175996	PANC-1	pancreas:	n/a	n/a
6	POLR2A	chr12:48174577-48176123	GM12892	blood:	n/a	n/a
7	POLR2A	chr12:48174528-48176247	GM12878	blood:	n/a	n/a
8	POLR2A	chr12:48174463-48176966	HUVEC	blood vessel:	n/a	n/a
9	POLR2A	chr12:48175281-48175869	Hela-S3	cervix:	n/a	n/a
10	POLR2A	chr12:48174495-48178624	ECC-1	luminal epithelium:	n/a	n/a
11	GATA3	chr12:48175368-48176101	T-47D	breast:	n/a	n/a
12	POLR2A	chr12:48175664-48176180	PANC-1	pancreas:	n/a	n/a
13	MTA3	chr12:48174801-48175832	GM12878	blood:	n/a	n/a
14	POLR2A	chr12:48168539-48189348	K562	blood:	n/a	n/a
15	POLR2A	chr12:48174698-48176170	GM12892	blood:	n/a	n/a
16	POLR2A	chr12:48174566-48182409	Hela-S3	cervix:	n/a	n/a
17	PML	chr12:48175009-48175942	K562	blood:	n/a	n/a
18	BCL3	chr12:48174975-48175930	A549	lung:	n/a	n/a
19	POLR2A	chr12:48174464-48176732	HUVEC	blood vessel:	n/a	n/a
20	POLR2A	chr12:48174560-48176569	U87	brain:	n/a	n/a
21	POLR2A	chr12:48174647-48178121	K562	blood:	n/a	n/a
22	POLR2A	chr12:48174558-48176397	SK-N-SH	brain:	n/a	n/a
23	POLR2A	chr12:48174622-48176936	HUVEC	blood vessel:	n/a	n/a
24	EP300	chr12:48175483-48176110	T-47D	breast:	n/a	n/a
25	POLR2A	chr12:48174570-48176017	A549	lung:	n/a	n/a
26	POLR2A	chr12:48174499-48178629	K562	blood:	n/a	n/a
27	POLR2A	chr12:48174596-48179981	K562	blood:	n/a	n/a
28	POLR2A	chr12:48175667-48175980	GM12891	blood:	n/a	n/a
29	POLR2A	chr12:48174592-48181015	K562	blood:	n/a	n/a
30	POLR2A	chr12:48174915-48175849	HCT-116	colon:	n/a	n/a
31	POLR2A	chr12:48174588-48177966	K562	blood:	n/a	n/a
32	POLR2A	chr12:48174624-48178557	K562	blood:	n/a	n/a
33	POLR2A	chr12:48172733-48176227	PFSK-1	brain:	n/a	n/a
34	POLR2A	chr12:48174676-48178288	A549	lung:	n/a	n/a
35	POLR2A	chr12:48174497-48176547	HUVEC	blood vessel:	n/a	n/a
36	JUND	chr12:48174581-48176082	A549	lung:	n/a	n/a
37	POLR2A	chr12:48174490-48178696	ECC-1	luminal epithelium:	n/a	n/a
38	POLR2A	chr12:48174562-48178245	Hela-S3	cervix:	n/a	n/a
39	POLR2A	chr12:48174708-48176058	GM12891	blood:	n/a	n/a
40	BCL3	chr12:48175534-48176136	K562	blood:	n/a	n/a
41	POLR2A	chr12:48175616-48176164	MCF10A-Er-Src	breast:	n/a	n/a
42	POLR2A	chr12:48174577-48175875	H1-hESC	embryonic stem cell:	n/a	n/a
43	POLR2A	chr12:48175431-48175851	A549	lung:	n/a	n/a
44	POLR2A	chr12:48175016-48176032	MCF-7	breast:	n/a	n/a
45	POLR2A	chr12:48174572-48176000	SK-N-MC	brain:	n/a	n/a
46	POLR2A	chr12:48174584-48176075	H1-hESC	embryonic stem cell:	n/a	n/a
47	POLR2A	chr12:48174465-48181100	K562	blood:	n/a	n/a
48	BCL3	chr12:48174572-48175842	A549	lung:	n/a	n/a
49	POLR2A	chr12:48174569-48175852	HUVEC	blood vessel:	n/a	n/a
50	POLR2A	chr12:48175533-48176012	GM12878	blood:	n/a	n/a

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:48173549..48176410-chr12:48184370..48186817,3	K562	blood:
2	chr12:48175695..48177408-chr12:48190225..48192647,2	K562	blood:
3	chr12:48164603..48170216-chr12:48170812..48178110,12	MCF-7	breast:
4	chr12:48175648..48178866-chr12:48181283..48184772,5	MCF-7	breast:
5	chr12:48173973..48175835-chr12:48212326..48213982,2	K562	blood:
6	chr12:48174794..48177034-chr12:48211084..48213999,3	MCF-7	breast:
7	chr12:48135925..48137862-chr12:48173853..48176277,2	MCF-7	breast:
8	chr12:48173992..48175896-chr12:48221117..48223369,2	MCF-7	breast:
9	chr12:48173236..48178017-chr12:48212091..48216621,8	MCF-7	breast:
10	chr12:48111607..48113554-chr12:48173778..48176264,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000268069	TF binding region
ENSG00000111405	Chromatin interaction
ENSG00000257488	Chromatin interaction
ENSG00000061273	Chromatin interaction
ENSG00000079337	Chromatin interaction
ENSG00000257433	Chromatin interaction
ENSG00000211584	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs2239190	0.85[EUR][1000 genomes]
rs3782908	1.00[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.99[ASN][1000 genomes]
rs7397585	0.92[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7399189	1.00[CEU][hapmap];0.89[MEX][hapmap];0.94[TSI][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs757342	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1813565	chr12:48097697-48177858	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer 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	39 gene(s)	inside rSNPs	diseases
2	nsv470289	chr12:48110551-48180508	Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Active TSS Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv1051941	chr12:48114026-48233128	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	75 gene(s)	inside rSNPs	diseases
4	nsv541487	chr12:48114026-48233128	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	75 gene(s)	inside rSNPs	diseases
5	nsv1036804	chr12:48114026-48287048	Enhancers Genic enhancers Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases
6	nsv524967	chr12:48119562-48215180	Flanking Active TSS Enhancers Genic enhancers Weak transcription Active TSS 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	66 gene(s)	inside rSNPs	diseases
7	nsv527470	chr12:48119955-48190166	Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
8	nsv899059	chr12:48129344-48215180	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases
9	nsv1052034	chr12:48146633-48287048	Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	78 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4760653	SENP1	cis	parietal	SCAN
rs4760653	BCDIN3D	cis	parietal	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:48168000-48177200	Weak transcription	Small Intestine	intestine
2	chr12:48168200-48195200	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr12:48168600-48178200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
4	chr12:48169000-48177600	Weak transcription	Dnd41	blood
5	chr12:48169200-48177600	Weak transcription	Fetal Lung	lung
6	chr12:48169200-48178600	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr12:48169400-48179200	Weak transcription	Fetal Kidney	kidney
8	chr12:48169800-48181200	Weak transcription	GM12878-XiMat	blood
9	chr12:48170600-48181200	Weak transcription	HepG2	liver
10	chr12:48172200-48175800	Weak transcription	Primary B cells from cord blood	blood
11	chr12:48172200-48177600	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr12:48172400-48175800	Weak transcription	HSMM	muscle
13	chr12:48172400-48176000	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr12:48172400-48176200	Weak transcription	HUVEC	blood vessel
15	chr12:48172400-48177400	Weak transcription	HSMMtube	muscle
16	chr12:48173000-48177000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr12:48173000-48177000	Weak transcription	Psoas Muscle	Psoas
18	chr12:48173000-48192400	Weak transcription	Right Atrium	heart
19	chr12:48173200-48175800	Weak transcription	Primary monocytes fromperipheralblood	blood
20	chr12:48173200-48176200	Weak transcription	Fetal Brain Male	brain
21	chr12:48173200-48176600	Weak transcription	HUES64 Cell Line	embryonic stem cell
22	chr12:48173200-48177600	Genic enhancers	Brain Substantia Nigra	brain
23	chr12:48173200-48177800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
24	chr12:48173200-48180400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr12:48173200-48191200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
26	chr12:48173400-48178000	Genic enhancers	Brain Inferior Temporal Lobe	brain
27	chr12:48173400-48180400	Strong transcription	Fetal Intestine Small	intestine
28	chr12:48173600-48175800	Weak transcription	Rectal Smooth Muscle	rectum
29	chr12:48173600-48176000	Weak transcription	Left Ventricle	heart
30	chr12:48173600-48176200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr12:48173600-48176400	Strong transcription	A549	lung
32	chr12:48173600-48176800	Weak transcription	Primary B cells from peripheral blood	blood
33	chr12:48173600-48177000	Genic enhancers	Brain Anterior Caudate	brain
34	chr12:48173600-48177200	Weak transcription	Primary T helper cells PMA-I stimulated	--
35	chr12:48173600-48178600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
36	chr12:48173600-48180400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
37	chr12:48173600-48187600	Weak transcription	Fetal Heart	heart
38	chr12:48173800-48175800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr12:48173800-48176000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr12:48173800-48176800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
41	chr12:48173800-48176800	Weak transcription	Colon Smooth Muscle	Colon
42	chr12:48173800-48176800	Strong transcription	Fetal Muscle Leg	muscle
43	chr12:48173800-48178000	Genic enhancers	Brain Hippocampus Middle	brain
44	chr12:48173800-48178200	Genic enhancers	Brain Cingulate Gyrus	brain
45	chr12:48173800-48178400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
46	chr12:48173800-48193800	Strong transcription	Gastric	stomach
47	chr12:48173800-48195400	Strong transcription	Fetal Stomach	stomach
48	chr12:48174000-48175800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
49	chr12:48174000-48177000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
50	chr12:48174000-48193000	Strong transcription	Placenta	Placenta

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