Variant report

Variant	rs569750716
Chromosome Location	chr12:49760672-49760673
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:363)
CpG islands
(count:0)
Chromatin interactive
region (count:48)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:363 , 50 per page) page: 1 2 3 4 5 6 7 8

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	HMGN3	chr12:49760157-49761591	K562	blood:	n/a	n/a
2	POLR2A	chr12:49760239-49761806	Hela-S3	cervix:	n/a	n/a
3	SIX5	chr12:49760108-49761102	A549	lung:	n/a	n/a
4	CEBPB	chr12:49760362-49761295	Hela-S3	cervix:	n/a	n/a
5	GABPA	chr12:49760197-49760776	K562	blood:	n/a	chr12:49760597-49760606 chr12:49760347-49760356
6	ELF1	chr12:49760204-49761409	MCF-7	breast:	n/a	chr12:49760356-49760368 chr12:49761322-49761334
7	NFIC	chr12:49760014-49761408	GM12878	blood:	n/a	n/a
8	MAX	chr12:49760130-49761428	H1-hESC	embryonic stem cell:	n/a	n/a
9	HEY1	chr12:49760125-49761424	HepG2	liver:	n/a	chr12:49760898-49760913 chr12:49760971-49760986 chr12:49760518-49760533
10	POLR2A	chr12:49760135-49761883	GM12878	blood:	n/a	n/a
11	SP4	chr12:49760369-49761282	H1-hESC	embryonic stem cell:	n/a	chr12:49761195-49761206
12	TAF1	chr12:49760226-49761429	K562	blood:	n/a	n/a
13	GATA3	chr12:49760022-49761395	MCF-7	breast:	n/a	chr12:49761286-49761296
14	ELF1	chr12:49760312-49760724	HepG2	liver:	n/a	chr12:49760356-49760368
15	POLR2A	chr12:49760150-49761454	Hela-S3	cervix:	n/a	n/a
16	POLR2A	chr12:49759832-49761928	HepG2	liver:	n/a	n/a
17	SIN3AK20	chr12:49760100-49761469	HCT-116	colon:	n/a	n/a
18	TBP	chr12:49760202-49761231	Hela-S3	cervix:	n/a	n/a
19	RELA	chr12:49760550-49761876	GM19099	blood:	n/a	n/a
20	POLR2A	chr12:49760440-49761960	H1-neurons	neurons:	n/a	n/a
21	TCF12	chr12:49759904-49761442	A549	lung:	n/a	n/a
22	ZBTB7A	chr12:49759978-49761950	ECC-1	luminal epithelium:	n/a	chr12:49760348-49760357 chr12:49760266-49760277
23	MAX	chr12:49760186-49761374	SK-N-SH	brain:	n/a	n/a
24	POU2F2	chr12:49760370-49760949	GM12891	blood:	n/a	n/a
25	TAL1	chr12:49760471-49761255	K562	blood:	n/a	n/a
26	YY1	chr12:49760263-49761440	A549	lung:	n/a	n/a
27	POLR2A	chr12:49760216-49761561	MCF-7	breast:	n/a	n/a
28	POLR2A	chr12:49760092-49761646	HUVEC	blood vessel:	n/a	n/a
29	CTCF	chr12:49760660-49760810	HepG2	liver:	n/a	n/a
30	SRF	chr12:49760498-49761448	ECC-1	luminal epithelium:	n/a	n/a
31	MYC	chr12:49760237-49761682	K562	blood:	n/a	n/a
32	POLR2A	chr12:49759876-49761869	HUVEC	blood vessel:	n/a	n/a
33	CTCF	chr12:49760540-49760690	HRPEpiC	eye:	n/a	n/a
34	POLR2A	chr12:49760303-49761416	GM12891	blood:	n/a	n/a
35	E2F6	chr12:49760071-49761083	H1-hESC	embryonic stem cell:	n/a	chr12:49760347-49760356 chr12:49761071-49761080 chr12:49761008-49761018 chr12:49761026-49761035 chr12:49760342-49760354 chr12:49760596-49760606
36	YY1	chr12:49760176-49761357	GM12892	blood:	n/a	n/a
37	SIN3A	chr12:49760085-49761782	H1-hESC	embryonic stem cell:	n/a	chr12:49760195-49760209 chr12:49760196-49760205
38	SIN3AK20	chr12:49760565-49761600	PANC-1	pancreas:	n/a	n/a
39	TAF1	chr12:49760397-49760737	PFSK-1	brain:	n/a	n/a
40	MAX	chr12:49760046-49761398	ECC-1	luminal epithelium:	n/a	n/a
41	POLR2A	chr12:49760305-49761514	HUVEC	blood vessel:	n/a	n/a
42	RCOR1	chr12:49760345-49761341	Hela-S3	cervix:	n/a	n/a
43	RUNX3	chr12:49759998-49762249	GM12878	blood:	n/a	n/a
44	REST	chr12:49760214-49761399	HL-60	blood:	n/a	chr12:49761322-49761335 chr12:49760355-49760368
45	MAZ	chr12:49760341-49761638	HepG2	liver:	n/a	n/a
46	CCNT2	chr12:49760244-49761501	K562	blood:	n/a	chr12:49760770-49760779 chr12:49761121-49761130
47	POLR2A	chr12:49760138-49761522	HepG2	liver:	n/a	n/a
48	BCLAF1	chr12:49760124-49761159	GM12878	blood:	n/a	chr12:49760690-49760703
49	POLR2A	chr12:49760184-49761716	GM18526	blood:	n/a	n/a
50	POLR2A	chr12:49759988-49761715	ECC-1	luminal epithelium:	n/a	n/a

No data

(count:48 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:49716623..49719210-chr12:49759055..49761901,3	MCF-7	breast:
2	chr12:49656837..49661590-chr12:49759665..49765017,7	K562	blood:
3	chr12:49657571..49662873-chr12:49757027..49762131,10	K562	blood:
4	chr12:49740569..49744952-chr12:49759719..49761508,3	K562	blood:
5	chr12:49689044..49692243-chr12:49760659..49764012,4	MCF-7	breast:
6	chr12:49729980..49732705-chr12:49760412..49762088,2	K562	blood:
7	chr1:249152247..249152996-chr12:49760452..49760979,2	Hela-S3	cervix:
8	chr1:210546877..210547690-chr12:49760648..49761536,2	Hela-S3	cervix:
9	chr12:49390072..49392510-chr12:49759241..49762093,2	K562	blood:
10	chr12:49759499..49761453-chr12:49953026..49955590,2	MCF-7	breast:
11	chr12:49759487..49762377-chr12:49960316..49963479,6	K562	blood:
12	chr12:49760226..49761054-chr6:26020583..26021188,2	Hela-S3	cervix:
13	chr12:49759658..49762377-chr12:49960316..49963047,2	K562	blood:
14	chr12:49758876..49762155-chr12:49906533..49909731,5	MCF-7	breast:
15	chr12:6579825..6580446-chr12:49760124..49760909,2	Hela-S3	cervix:
16	chr12:49717382..49719680-chr12:49758980..49761177,3	K562	blood:
17	chr12:49758243..49761237-chr12:50135535..50137212,2	MCF-7	breast:
18	chr1:178062063..178062911-chr12:49760494..49761260,2	Hela-S3	cervix:
19	chr12:49757911..49761864-chr12:50015854..50019350,3	K562	blood:
20	chr12:49759096..49761213-chr12:49881834..49884299,3	K562	blood:
21	chr12:49759519..49761735-chr12:49853453..49856491,3	K562	blood:
22	chr12:3067959..3068514-chr12:49760628..49761230,2	Hela-S3	cervix:
23	chr12:49758102..49760925-chr12:49950793..49953218,2	MCF-7	breast:
24	chr12:49759638..49761406-chr12:49937675..49939250,2	MCF-7	breast:
25	chr12:49760412..49761224-chr3:49058710..49059332,2	Hela-S3	cervix:
26	chr12:49759045..49761163-chr12:50015602..50018404,2	MCF-7	breast:
27	chr12:49759192..49762198-chr12:50016828..50018696,3	MCF-7	breast:
28	chr12:49760469..49761279-chr7:35077075..35077749,2	HCT-116	colon:
29	chr12:49760432..49761123-chr12:56123061..56123918,2	Hela-S3	cervix:
30	chr12:49745336..49748188-chr12:49759488..49762139,2	K562	blood:
31	chr1:45987092..45987937-chr12:49760616..49761183,2	Hela-S3	cervix:
32	chr12:49759029..49763168-chr12:49779946..49784312,5	MCF-7	breast:
33	chr12:49729980..49733163-chr12:49759007..49762779,4	K562	blood:
34	chr12:49760076..49762481-chr12:49958970..49962083,4	MCF-7	breast:
35	chr12:49760568..49761364-chr7:100303129..100303747,2	NB4	blood:
36	chr12:49760156..49760721-chr2:157198454..157199445,2	Hela-S3	cervix:
37	chr12:49757995..49761023-chr12:49883452..49885795,3	MCF-7	breast:
38	chr12:49760593..49761565-chr3:183979036..183979812,2	Hela-S3	cervix:
39	chr12:49740075..49745225-chr12:49756992..49761732,8	K562	blood:
40	chr12:49760364..49760986-chr16:57480845..57481573,2	Hela-S3	cervix:
41	chr12:49760414..49761059-chr22:38597972..38598890,2	Hela-S3	cervix:
42	chr12:49759421..49761447-chr17:56735493..56738018,2	MCF-7	breast:
43	chr12:49759353..49761548-chr12:49931777..49934189,4	K562	blood:
44	chr12:49759353..49762276-chr12:49930939..49933731,4	K562	blood:
45	chr12:49759570..49762166-chr12:49852805..49855688,2	MCF-7	breast:
46	chr12:49739131..49745064-chr12:49758784..49762517,10	MCF-7	breast:
47	chr12:49740264..49744957-chr12:49759411..49762039,7	MCF-7	breast:
48	chr12:49730111..49734791-chr12:49758969..49762593,4	MCF-7	breast:

No data

Variant related genes	Relation type
SPATS2	TF binding region
ENSG00000172336	Chromatin interaction
ENSG00000202077	Chromatin interaction
ENSG00000187778	Chromatin interaction
ENSG00000178401	Chromatin interaction
ENSG00000200972	Chromatin interaction
ENSG00000185022	Chromatin interaction
ENSG00000075391	Chromatin interaction
ENSG00000153234	Chromatin interaction
ENSG00000186897	Chromatin interaction
ENSG00000163888	Chromatin interaction
ENSG00000167553	Chromatin interaction
ENSG00000224687	Chromatin interaction
ENSG00000197905	Chromatin interaction
ENSG00000173852	Chromatin interaction
ENSG00000258334	Chromatin interaction
ENSG00000135519	Chromatin interaction
ENSG00000117450	Chromatin interaction
ENSG00000258101	Chromatin interaction
ENSG00000123352	Chromatin interaction
ENSG00000110844	Chromatin interaction
ENSG00000135451	Chromatin interaction
ENSG00000171163	Chromatin interaction
ENSG00000139644	Chromatin interaction
ENSG00000139190	Chromatin interaction
ENSG00000178057	Chromatin interaction
ENSG00000257954	Chromatin interaction
ENSG00000257913	Chromatin interaction
ENSG00000005194	Chromatin interaction
ENSG00000135406	Chromatin interaction
ENSG00000198366	Chromatin interaction
ENSG00000088682	Chromatin interaction
ENSG00000135404	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 0)

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	nsv1051161	chr12:49314550-49828473	Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Active TSS Strong transcription Enhancers Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	322 gene(s)	inside rSNPs	diseases
2	nsv541489	chr12:49314550-49828473	Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	322 gene(s)	inside rSNPs	diseases
3	nsv1036452	chr12:49376285-49867760	Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	315 gene(s)	inside rSNPs	diseases
4	nsv1042122	chr12:49678529-49823168	Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Enhancers Active TSS Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases
5	nsv1039176	chr12:49678529-49832618	Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	55 gene(s)	inside rSNPs	diseases
6	nsv899068	chr12:49714103-49924637	Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
7	nsv832405	chr12:49720279-49910862	Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
8	esv3423651	chr12:49760110-49762658	Active TSS Flanking Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
9	nsv899069	chr12:49760499-49924637	Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:49759600-49762000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr12:49759600-49762000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr12:49759600-49762200	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr12:49759600-49762600	Active TSS	H1 Cell Line	embryonic stem cell
5	chr12:49759600-49762600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr12:49759600-49763000	Active TSS	A549	lung
7	chr12:49759800-49761000	Enhancers	Fetal Brain Male	brain
8	chr12:49759800-49761600	Active TSS	Placenta	Placenta
9	chr12:49759800-49761600	Active TSS	Rectal Mucosa Donor 31	rectum
10	chr12:49759800-49761600	Active TSS	Rectal Smooth Muscle	rectum
11	chr12:49759800-49761800	Active TSS	iPS-18 Cell Line	embryonic stem cell
12	chr12:49759800-49761800	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr12:49759800-49761800	Active TSS	Cortex derived primary cultured neurospheres	brain
14	chr12:49759800-49761800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr12:49759800-49761800	Active TSS	Hela-S3	cervix
16	chr12:49759800-49762000	Active TSS	ES-I3 Cell Line	embryonic stem cell
17	chr12:49759800-49762000	Active TSS	HUES48 Cell Line	embryonic stem cell
18	chr12:49759800-49762000	Active TSS	HUES64 Cell Line	embryonic stem cell
19	chr12:49759800-49762000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr12:49759800-49762200	Active TSS	H9 Cell Line	embryonic stem cell
21	chr12:49759800-49762200	Active TSS	Colonic Mucosa	Colon
22	chr12:49759800-49762200	Active TSS	Fetal Intestine Large	intestine
23	chr12:49759800-49762400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr12:49759800-49762600	Active TSS	HSMM	muscle
25	chr12:49759800-49763200	Active TSS	GM12878-XiMat	blood
26	chr12:49759800-49764000	Active TSS	Rectal Mucosa Donor 29	rectum
27	chr12:49760000-49760800	Active TSS	Fetal Heart	heart
28	chr12:49760000-49761200	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
29	chr12:49760000-49761600	Active TSS	Primary T helper naive cells from peripheral blood	blood
30	chr12:49760000-49761600	Active TSS	Primary T regulatory cells fromperipheralblood	blood
31	chr12:49760000-49761600	Active TSS	Liver	Liver
32	chr12:49760000-49761600	Active TSS	Duodenum Mucosa	Duodenum
33	chr12:49760000-49761800	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
34	chr12:49760000-49761800	Active TSS	Brain Cingulate Gyrus	brain
35	chr12:49760000-49761800	Active TSS	Brain Hippocampus Middle	brain
36	chr12:49760000-49761800	Active TSS	Fetal Lung	lung
37	chr12:49760000-49761800	Active TSS	Placenta Amnion	Placenta Amnion
38	chr12:49760000-49761800	Active TSS	Stomach Mucosa	stomach
39	chr12:49760000-49762000	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr12:49760000-49762000	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr12:49760000-49762000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr12:49760000-49762000	Active TSS	HUES6 Cell Line	embryonic stem cell
43	chr12:49760000-49762000	Active TSS	iPS-15b Cell Line	embryonic stem cell
44	chr12:49760000-49762000	Active TSS	iPS-20b Cell Line	embryonic stem cell
45	chr12:49760000-49762000	Active TSS	Aorta	Aorta
46	chr12:49760000-49762000	Active TSS	Brain Substantia Nigra	brain
47	chr12:49760000-49762000	Active TSS	Colon Smooth Muscle	Colon
48	chr12:49760000-49762000	Active TSS	Duodenum Smooth Muscle	Duodenum
49	chr12:49760000-49762000	Active TSS	Esophagus	oesophagus
50	chr12:49760000-49762000	Active TSS	Gastric	stomach

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links