Variant report

Variant	rs59811639
Chromosome Location	chr12:56695954-56695955
allele	C/T
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	FOXA2	chr12:56695525-56695967	HepG2	liver:	n/a	n/a
2	NR2F2	chr12:56693066-56696557	K562	blood:	n/a	n/a
3	RAD21	chr12:56695706-56696564	SK-N-SH	brain:	n/a	chr12:56696322-56696336 chr12:56696318-56696337
4	HDAC2	chr12:56695435-56696044	HepG2	liver:	n/a	n/a
5	RCOR1	chr12:56695616-56696348	HepG2	liver:	n/a	n/a
6	MXI1	chr12:56695613-56696362	HepG2	liver:	n/a	n/a
7	NR2F2	chr12:56695388-56696344	HepG2	liver:	n/a	n/a
8	NFIC	chr12:56695408-56696125	HepG2	liver:	n/a	n/a
9	POLR2A	chr12:56695934-56696332	Hela-S3	cervix:	n/a	n/a
10	NR2F2	chr12:56695329-56696549	HepG2	liver:	n/a	n/a
11	FOXA1	chr12:56695448-56696075	HepG2	liver:	n/a	n/a
12	CTCF	chr12:56695900-56696050	GM12878	blood:	n/a	n/a
13	JUND	chr12:56695463-56695965	HepG2	liver:	n/a	n/a
14	TEAD4	chr12:56695373-56696539	HepG2	liver:	n/a	n/a
15	RAD21	chr12:56695924-56696694	HCT-116	colon:	n/a	chr12:56696322-56696336 chr12:56696318-56696337
16	HEY1	chr12:56695408-56696384	HepG2	liver:	n/a	chr12:56695717-56695726
17	POLR2A	chr12:56695792-56696132	HepG2	liver:	n/a	n/a
18	CTCF	chr12:56695951-56696723	HCT-116	colon:	n/a	chr12:56696321-56696337 chr12:56696315-56696336 chr12:56696320-56696338 chr12:56696326-56696335 chr12:56696322-56696335
19	RXRA	chr12:56695482-56696037	HepG2	liver:	n/a	chr12:56695572-56695581 chr12:56695978-56695997
20	CTCF	chr12:56695763-56696742	SK-N-SH	brain:	n/a	chr12:56696321-56696337 chr12:56696315-56696336 chr12:56696320-56696338 chr12:56696326-56696335 chr12:56696322-56696335
21	ARID3A	chr12:56695578-56696488	HepG2	liver:	n/a	n/a
22	RAD21	chr12:56695613-56696493	HepG2	liver:	n/a	chr12:56696322-56696336 chr12:56696318-56696337
23	CTCF	chr12:56695860-56696010	HAc	cerebellar:	n/a	n/a
24	MYBL2	chr12:56695374-56696449	HepG2	liver:	n/a	n/a
25	POLR2A	chr12:56695464-56696382	HepG2	liver:	n/a	n/a
26	RAD21	chr12:56695715-56696507	HepG2	liver:	n/a	chr12:56696322-56696336 chr12:56696318-56696337
27	SMC3	chr12:56695634-56696491	HepG2	liver:	n/a	chr12:56696322-56696336
28	CTCF	chr12:56695635-56696796	A549	lung:	n/a	chr12:56696321-56696337 chr12:56696315-56696336 chr12:56696320-56696338 chr12:56696326-56696335 chr12:56696322-56696335
29	POLR2A	chr12:56695814-56696276	ECC-1	luminal epithelium:	n/a	n/a
30	MBD4	chr12:56695355-56696434	HepG2	liver:	n/a	n/a
31	POLR2A	chr12:56695253-56696410	HepG2	liver:	n/a	n/a
32	CEBPB	chr12:56695571-56695964	HepG2	liver:	n/a	n/a
33	NFIC	chr12:56695331-56696381	HepG2	liver:	n/a	n/a
34	HNF4G	chr12:56695516-56696016	HepG2	liver:	n/a	chr12:56695857-56695865
35	RAD21	chr12:56695887-56696664	HCT-116	colon:	n/a	chr12:56696322-56696336 chr12:56696318-56696337
36	POLR2A	chr12:56695556-56696552	SK-N-MC	brain:	n/a	n/a
37	ESRRA	chr12:56695561-56696724	GM12878	blood:	n/a	chr12:56696271-56696289 chr12:56696281-56696293 chr12:56696273-56696287 chr12:56696281-56696291 chr12:56696282-56696300 chr12:56696272-56696288
38	MAZ	chr12:56695584-56696449	HepG2	liver:	n/a	n/a
39	BRCA1	chr12:56695652-56696274	HepG2	liver:	n/a	n/a
40	SP1	chr12:56695331-56696394	HepG2	liver:	n/a	n/a
41	FOXA1	chr12:56695388-56696084	HepG2	liver:	n/a	n/a
42	CTCF	chr12:56695820-56695970	A549	lung:	n/a	n/a
43	POLR2A	chr12:56692938-56696691	HepG2	liver:	n/a	n/a
44	MYBL2	chr12:56695303-56696430	HepG2	liver:	n/a	n/a
45	RXRA	chr12:56695380-56696107	HepG2	liver:	n/a	chr12:56695572-56695581 chr12:56695978-56695997
46	CEBPB	chr12:56695528-56695966	HepG2	liver:	n/a	n/a
47	CTCF	chr12:56695860-56696010	HCFaa	heart:	n/a	n/a
48	HDAC2	chr12:56695488-56696331	HepG2	liver:	n/a	n/a
49	HEY1	chr12:56695337-56696333	HepG2	liver:	n/a	chr12:56695717-56695726
50	POLR2A	chr12:56695493-56696271	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:56659486..56662634-chr12:56692106..56696696,6	MCF-7	breast:
2	chr12:56435468..56437513-chr12:56694751..56696296,2	K562	blood:
3	chr12:56692256..56696973-chr12:56707335..56712231,9	K562	blood:
4	chr12:56690986..56698275-chr12:56706607..56711958,20	MCF-7	breast:
5	chr12:56652045..56652731-chr12:56695880..56696766,2	MCF-7	breast:
6	chr12:56652145..56655661-chr12:56692434..56696303,4	MCF-7	breast:
7	chr12:56690402..56700610-chr12:56705161..56712229,20	K562	blood:
8	chr12:56693116..56697525-chr12:56726716..56730598,5	K562	blood:
9	chr12:56650147..56652111-chr12:56693703..56696656,2	MCF-7	breast:
10	chr12:56695752..56697519-chr12:56726820..56729640,2	MCF-7	breast:
11	chr12:56617925..56618696-chr12:56695888..56696814,2	K562	blood:
12	chr12:56692603..56696463-chr12:56860417..56864951,8	K562	blood:
13	chr12:56679574..56682384-chr12:56692383..56696875,5	K562	blood:
14	chr12:56694767..56697892-chr12:56702654..56704783,4	K562	blood:
15	chr12:56660112..56662081-chr12:56694632..56696387,3	K562	blood:
16	chr12:56694327..56696089-chr12:56861619..56863910,2	MCF-7	breast:
17	chr12:56509513..56513531-chr12:56694540..56697702,5	K562	blood:
18	chr12:56694994..56697860-chr12:56698216..56699984,2	MCF-7	breast:
19	chr12:56693640..56697163-chr12:56700934..56704368,3	MCF-7	breast:
20	chr12:56679574..56681804-chr12:56694461..56697113,2	K562	blood:
21	chr12:56509293..56514359-chr12:56692717..56696999,9	K562	blood:
22	chr12:56650670..56653389-chr12:56691740..56696063,7	MCF-7	breast:
23	chr12:56615624..56617857-chr12:56693691..56696506,3	K562	blood:
24	chr12:56692746..56696004-chr12:56729098..56732987,4	K562	blood:
25	chr12:56585782..56587966-chr12:56695653..56698357,2	K562	blood:
26	chr12:56625939..56627578-chr12:56694733..56696853,2	K562	blood:
27	chr12:56692603..56696463-chr12:56860417..56864951,9	K562	blood:
28	chr12:56695853..56696434-chr12:56857361..56858155,2	K562	blood:
29	chr12:56514975..56517772-chr12:56694804..56696732,2	MCF-7	breast:
30	chr12:56497940..56500843-chr12:56693833..56696028,2	K562	blood:
31	chr12:56694315..56696135-chr12:56730935..56732987,2	K562	blood:
32	chr12:56658873..56662296-chr12:56692937..56696387,6	K562	blood:

Variant related genes	Relation type
CS	TF binding region
ENSG00000110944	Chromatin interaction
ENSG00000197728	Chromatin interaction
ENSG00000139579	Chromatin interaction
ENSG00000135473	Chromatin interaction
ENSG00000139641	Chromatin interaction
ENSG00000258345	Chromatin interaction
ENSG00000257449	Chromatin interaction
ENSG00000135517	Chromatin interaction
ENSG00000135469	Chromatin interaction
ENSG00000135482	Chromatin interaction
ENSG00000176422	Chromatin interaction
ENSG00000170515	Chromatin interaction
ENSG00000144785	Chromatin interaction
ENSG00000257727	Chromatin interaction
ENSG00000181852	Chromatin interaction
ENSG00000257740	Chromatin interaction
ENSG00000139645	Chromatin interaction
ENSG00000062485	Chromatin interaction
ENSG00000229117	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10876882	0.81[EUR][1000 genomes]
rs11171803	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11171806	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11575224	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11575229	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11575231	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11575232	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11575234	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11575248	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1274490	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1274493	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1295772	0.91[ASN][1000 genomes]
rs17118403	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17118409	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17118431	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17118439	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1802236	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2020854	0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2066807	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2066808	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2066818	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2066819	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2291361	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2306693	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2306694	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2371454	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2371494	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2629447	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2643623	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2643626	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2695782	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2695788	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2695789	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35526714	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs41392645	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41423244	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57137641	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57279772	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57343616	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs57367440	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs57870697	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs58852079	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59295315	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59626664	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs59822547	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs59917308	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs60192809	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60542959	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs60913149	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs703830	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs744051	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs773652	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs773664	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs773665	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs808919	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs871130	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1043622	chr12:56571476-56974448	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	95 gene(s)	inside rSNPs	diseases
2	nsv541500	chr12:56571476-56974448	Weak transcription Strong transcription Bivalent/Poised TSS Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	95 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs59811639	RP11-977G19.11	cis	Artery Aorta	GTEx
rs59811639	TMEM4	Cis_1M	lymphoblastoid	RTeQTL
rs59811639	RP11-977G19.11	cis	Artery Tibial	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:56694400-56696200	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
2	chr12:56694600-56696000	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
3	chr12:56694600-56704400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr12:56694600-56708400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr12:56694800-56696200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
6	chr12:56694800-56696200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
7	chr12:56694800-56696200	Enhancers	Pancreas	Pancrea
8	chr12:56694800-56696400	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
9	chr12:56694800-56696600	Enhancers	Primary B cells from cord blood	blood
10	chr12:56694800-56696600	Enhancers	Primary T helper cells PMA-I stimulated	--
11	chr12:56694800-56696600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
12	chr12:56694800-56696800	Enhancers	Primary T cells fromperipheralblood	blood
13	chr12:56694800-56697200	Enhancers	Primary B cells from peripheral blood	blood
14	chr12:56694800-56697600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr12:56694800-56708200	Weak transcription	Pancreatic Islets	Pancreatic Islet
16	chr12:56694800-56708800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
17	chr12:56695000-56696000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr12:56695000-56696000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
19	chr12:56695000-56696000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
20	chr12:56695000-56696000	Enhancers	Fetal Intestine Large	intestine
21	chr12:56695000-56696200	Enhancers	Primary T cells from cord blood	blood
22	chr12:56695000-56696200	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr12:56695000-56696200	Enhancers	Brain Anterior Caudate	brain
24	chr12:56695000-56696200	Enhancers	Fetal Thymus	thymus
25	chr12:56695000-56696200	Enhancers	Rectal Mucosa Donor 31	rectum
26	chr12:56695000-56696400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
27	chr12:56695000-56696400	Enhancers	Primary T helper naive cells from peripheral blood	blood
28	chr12:56695000-56696400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
29	chr12:56695000-56696400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
30	chr12:56695000-56696400	Enhancers	Primary T killer memory cells from peripheral blood	blood
31	chr12:56695000-56696400	Enhancers	Brain Substantia Nigra	brain
32	chr12:56695000-56696400	Enhancers	Duodenum Smooth Muscle	Duodenum
33	chr12:56695000-56696400	Enhancers	Rectal Smooth Muscle	rectum
34	chr12:56695000-56696400	Enhancers	Stomach Mucosa	stomach
35	chr12:56695000-56696800	Enhancers	Primary T helper cells fromperipheralblood	blood
36	chr12:56695000-56697000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
37	chr12:56695000-56697200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr12:56695000-56697200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
39	chr12:56695000-56697200	Weak transcription	Fetal Brain Female	brain
40	chr12:56695000-56697800	Weak transcription	Sigmoid Colon	Sigmoid Colon
41	chr12:56695000-56698000	Weak transcription	HUES6 Cell Line	embryonic stem cell
42	chr12:56695000-56698200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr12:56695000-56698600	Weak transcription	Brain Angular Gyrus	brain
44	chr12:56695000-56699000	Weak transcription	NH-A	brain
45	chr12:56695000-56700400	Weak transcription	Brain Germinal Matrix	brain
46	chr12:56695000-56700400	Weak transcription	Thymus	Thymus
47	chr12:56695000-56701800	Weak transcription	Ovary	ovary
48	chr12:56695000-56702000	Weak transcription	Placenta Amnion	Placenta Amnion
49	chr12:56695000-56702800	Weak transcription	Small Intestine	intestine
50	chr12:56695000-56703600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell

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