Variant report

Variant	rs833842
Chromosome Location	chr12:49365423-49365424
allele	G/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	CTBP2	chr12:49362803-49365797	H1-hESC	embryonic stem cell:	n/a	n/a
2	MYC	chr12:49364982-49365710	K562	blood:	n/a	chr12:49365173-49365183
3	TCF7L2	chr12:49365038-49365763	HCT-116	colon:	n/a	n/a
4	SUZ12	chr12:49363798-49366856	H1-hESC	embryonic stem cell:	n/a	n/a
5	MAX	chr12:49364875-49365838	K562	blood:	n/a	chr12:49365173-49365183
6	CTCF	chr12:49365320-49365470	HCPEpiC	choroid plexus:	n/a	n/a
7	MAX	chr12:49364802-49365543	Hela-S3	cervix:	n/a	chr12:49364858-49364868 chr12:49365173-49365183
8	UBTF	chr12:49365261-49365550	K562	blood:	n/a	n/a
9	MAX	chr12:49364929-49365923	A549	lung:	n/a	chr12:49365173-49365183
10	E2F6	chr12:49365054-49365525	K562	blood:	n/a	n/a
11	SPI1	chr12:49365302-49365521	K562	blood:	n/a	n/a
12	MAX	chr12:49364950-49365448	Hela-S3	cervix:	n/a	chr12:49365173-49365183
13	MAX	chr12:49364845-49367135	NB4	blood:	n/a	chr12:49364858-49364868 chr12:49365173-49365183 chr12:49366530-49366539
14	MAZ	chr12:49365251-49365585	K562	blood:	n/a	n/a
15	HMGN3	chr12:49365305-49365643	K562	blood:	n/a	n/a
16	CTCF	chr12:49365380-49365530	Caco-2	colon:	n/a	n/a
17	POLR2A	chr12:49365076-49365600	H1-neurons	neurons:	n/a	n/a
18	MAZ	chr12:49364909-49365992	IMR90	lung:	n/a	n/a
19	SIN3A	chr12:49365121-49365738	H1-hESC	embryonic stem cell:	n/a	n/a
20	HEY1	chr12:49365417-49365624	K562	blood:	n/a	n/a
21	UBTF	chr12:49364996-49365649	K562	blood:	n/a	n/a
22	ZNF143	chr12:49365401-49365631	H1-hESC	embryonic stem cell:	n/a	n/a
23	HA-E2F1	chr12:49365327-49365910	MCF-7	breast:	n/a	n/a
24	MAZ	chr12:49365125-49365482	Hela-S3	cervix:	n/a	n/a
25	MAX	chr12:49364367-49365979	A549	lung:	n/a	chr12:49364858-49364868 chr12:49365173-49365183
26	POLR2A	chr12:49365082-49365679	PFSK-1	brain:	n/a	n/a
27	MAZ	chr12:49365334-49365634	GM12878	blood:	n/a	n/a
28	POLR2A	chr12:49365369-49365702	K562	blood:	n/a	n/a
29	POLR2A	chr12:49365224-49365674	ECC-1	luminal epithelium:	n/a	n/a
30	MXI1	chr12:49364764-49365622	SK-N-SH	brain:	n/a	n/a
31	MAX	chr12:49364826-49365548	ECC-1	luminal epithelium:	n/a	chr12:49364858-49364868 chr12:49365173-49365183
32	POLR2A	chr12:49365301-49365807	HCT-116	colon:	n/a	n/a
33	MAX	chr12:49364629-49366074	HCT-116	colon:	n/a	chr12:49364858-49364868 chr12:49365173-49365183
34	TBP	chr12:49365358-49365626	H1-hESC	embryonic stem cell:	n/a	n/a
35	ZNF263	chr12:49364568-49366429	HEK293-T-REx	kidney:	n/a	chr12:49365412-49365433 chr12:49364910-49364919 chr12:49364753-49364762 chr12:49365612-49365621
36	MAX	chr12:49364870-49365948	ECC-1	luminal epithelium:	n/a	chr12:49365173-49365183
37	POLR2A	chr12:49364956-49365849	PFSK-1	brain:	n/a	n/a
38	POLR2A	chr12:49365039-49365629	H1-neurons	neurons:	n/a	n/a
39	POLR2A	chr12:49365281-49365768	K562	blood:	n/a	n/a
40	SPI1	chr12:49365144-49365621	HL-60	blood:	n/a	n/a
41	MYC	chr12:49364997-49366825	NB4	blood:	n/a	chr12:49365173-49365183 chr12:49366530-49366539
42	MAX	chr12:49364631-49365634	MCF-7	breast:	n/a	chr12:49364858-49364868 chr12:49365173-49365183
43	E2F6	chr12:49364936-49365733	K562	blood:	n/a	n/a
44	MAX	chr12:49365015-49365617	H1-hESC	embryonic stem cell:	n/a	chr12:49365173-49365183
45	MAX	chr12:49364757-49365939	HCT-116	colon:	n/a	chr12:49364858-49364868 chr12:49365173-49365183

No.	Distal block	Cell Line	Cell type
1	chr12:49351084..49352752-chr12:49363357..49365742,2	K562	blood:
2	chr12:49348867..49353149-chr12:49362475..49369316,15	MCF-7	breast:
3	chr12:49347357..49351835-chr12:49360389..49366684,9	MCF-7	breast:
4	chr12:49365267..49367565-chr12:49453514..49456197,2	K562	blood:
5	chr12:49365293..49369225-chr12:49386844..49389863,3	MCF-7	breast:

Variant related genes	Relation type
RNU6-940P	TF binding region
WNT10B	TF binding region
ENSG00000167548	Chromatin interaction
ENSG00000134287	Chromatin interaction
ENSG00000258283	Chromatin interaction
ENSG00000272822	Chromatin interaction

Extended variants
information (count: 118 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:114)

rs_ID	r²[population]
rs1051886	0.89[ASN][1000 genomes]
rs1054376	0.87[ASN][1000 genomes]
rs10747556	0.83[ASN][1000 genomes]
rs10747557	0.87[ASN][1000 genomes]
rs10747558	0.88[ASN][1000 genomes]
rs10783289	0.83[ASN][1000 genomes]
rs10783293	0.83[ASN][1000 genomes]
rs10783294	0.83[ASN][1000 genomes]
rs10783295	0.83[ASN][1000 genomes]
rs10783297	0.87[ASN][1000 genomes]
rs10875886	0.83[ASN][1000 genomes]
rs10875893	0.81[ASN][1000 genomes]
rs10875894	0.83[ASN][1000 genomes]
rs10875895	0.83[ASN][1000 genomes]
rs10875896	0.80[ASN][1000 genomes]
rs10875897	0.87[ASN][1000 genomes]
rs10875898	0.87[ASN][1000 genomes]
rs10875899	0.81[ASN][1000 genomes]
rs10875900	0.89[ASN][1000 genomes]
rs10875901	0.88[ASN][1000 genomes]
rs10875902	0.89[ASN][1000 genomes]
rs1111662	0.88[ASN][1000 genomes]
rs11168779	0.82[ASN][1000 genomes]
rs11168783	0.83[ASN][1000 genomes]
rs11168784	0.82[ASN][1000 genomes]
rs11168785	0.83[ASN][1000 genomes]
rs11168790	0.83[ASN][1000 genomes]
rs11168792	0.85[ASN][1000 genomes]
rs11168794	0.85[ASN][1000 genomes]
rs11168795	0.88[ASN][1000 genomes]
rs11168797	0.88[ASN][1000 genomes]
rs11168798	0.83[ASN][1000 genomes]
rs11168800	0.83[ASN][1000 genomes]
rs11168801	0.83[ASN][1000 genomes]
rs11168803	0.89[ASN][1000 genomes]
rs11168811	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11168812	0.90[ASN][1000 genomes]
rs11608916	0.84[ASN][1000 genomes]
rs11610459	0.83[ASN][1000 genomes]
rs11610497	0.83[ASN][1000 genomes]
rs11614474	0.83[ASN][1000 genomes]
rs12227240	0.80[ASN][1000 genomes]
rs12228521	0.83[ASN][1000 genomes]
rs12229275	0.83[ASN][1000 genomes]
rs12423542	0.85[ASN][1000 genomes]
rs12579249	0.83[ASN][1000 genomes]
rs1318692	0.82[ASN][1000 genomes]
rs1690182	0.89[ASN][1000 genomes]
rs1818996	0.87[ASN][1000 genomes]
rs1830192	0.87[ASN][1000 genomes]
rs2030900	0.88[ASN][1000 genomes]
rs2070940	0.88[ASN][1000 genomes]
rs2073480	0.88[ASN][1000 genomes]
rs2131713	0.87[ASN][1000 genomes]
rs2272311	0.86[ASN][1000 genomes]
rs2272312	0.84[ASN][1000 genomes]
rs2293449	0.85[ASN][1000 genomes]
rs2368701	0.83[ASN][1000 genomes]
rs2453063	0.89[ASN][1000 genomes]
rs2463175	0.88[ASN][1000 genomes]
rs2641450	0.86[ASN][1000 genomes]
rs2694839	0.88[ASN][1000 genomes]
rs2694840	0.86[ASN][1000 genomes]
rs3741627	0.89[ASN][1000 genomes]
rs3759146	0.84[ASN][1000 genomes]
rs3782353	0.89[ASN][1000 genomes]
rs3809147	0.82[ASN][1000 genomes]
rs3825182	0.84[ASN][1000 genomes]
rs3825184	0.82[ASN][1000 genomes]
rs4018510	0.87[ASN][1000 genomes]
rs4237854	0.85[ASN][1000 genomes]
rs4433614	0.82[ASN][1000 genomes]
rs4526804	0.88[ASN][1000 genomes]
rs4760600	0.83[ASN][1000 genomes]
rs4760661	0.84[ASN][1000 genomes]
rs4760662	0.91[ASN][1000 genomes]
rs4760663	0.94[ASN][1000 genomes]
rs4760664	0.88[ASN][1000 genomes]
rs4760665	0.83[ASN][1000 genomes]
rs4760666	0.86[ASN][1000 genomes]
rs4760667	0.87[ASN][1000 genomes]
rs4760668	0.89[ASN][1000 genomes]
rs58023472	0.83[ASN][1000 genomes]
rs59087236	0.88[ASN][1000 genomes]
rs61941142	0.82[ASN][1000 genomes]
rs61942166	0.87[ASN][1000 genomes]
rs61942167	0.88[ASN][1000 genomes]
rs61942169	0.89[ASN][1000 genomes]
rs61942207	0.88[ASN][1000 genomes]
rs61942209	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6580696	0.89[ASN][1000 genomes]
rs7297958	0.83[ASN][1000 genomes]
rs7298330	0.83[ASN][1000 genomes]
rs7304942	0.83[ASN][1000 genomes]
rs7313988	0.88[ASN][1000 genomes]
rs7963018	0.89[ASN][1000 genomes]
rs7963160	0.89[ASN][1000 genomes]
rs7976473	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs833820	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs833821	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs833822	0.88[ASN][1000 genomes]
rs833827	0.88[ASN][1000 genomes]
rs833828	0.86[ASN][1000 genomes]
rs833839	0.82[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs833840	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs833841	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs833843	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs961320	0.82[ASN][1000 genomes]
rs9645813	0.82[ASN][1000 genomes]
rs9783452	0.88[ASN][1000 genomes]
rs9783477	0.88[ASN][1000 genomes]
rs9788029	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9795742	0.81[ASN][1000 genomes]
rs9796008	0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832404	chr12:49258560-49458555	Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
2	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
3	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
4	nsv558833	chr12:49358880-49478812	Bivalent Enhancer Flanking Active TSS Enhancers Strong transcription Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs833842	CCDC65	cis	Esophagus Muscularis	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:49362800-49366000	Bivalent Enhancer	Fetal Intestine Large	intestine
2	chr12:49363000-49366000	Enhancers	Pancreas	Pancrea
3	chr12:49363200-49365800	Bivalent Enhancer	Primary B cells from cord blood	blood
4	chr12:49363200-49366200	Bivalent Enhancer	Stomach Mucosa	stomach
5	chr12:49363400-49366200	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
6	chr12:49363600-49366000	Bivalent Enhancer	Fetal Heart	heart
7	chr12:49363600-49368000	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
8	chr12:49363800-49365800	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr12:49363800-49366200	Bivalent Enhancer	Primary neutrophils fromperipheralblood	blood
10	chr12:49364000-49365600	Bivalent Enhancer	Liver	Liver
11	chr12:49364000-49366000	Bivalent Enhancer	Spleen	Spleen
12	chr12:49364200-49365600	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
13	chr12:49364200-49365600	Weak transcription	Gastric	stomach
14	chr12:49364200-49365800	Bivalent Enhancer	Fetal Lung	lung
15	chr12:49364200-49366000	Bivalent Enhancer	Brain Substantia Nigra	brain
16	chr12:49364200-49366600	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
17	chr12:49364200-49368000	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
18	chr12:49364400-49365800	Flanking Bivalent TSS/Enh	Adipose Nuclei	Adipose
19	chr12:49364400-49366400	Bivalent Enhancer	Primary B cells from peripheral blood	blood
20	chr12:49364400-49366400	Bivalent Enhancer	Primary T killer naive cells fromperipheralblood	blood
21	chr12:49364600-49365800	Flanking Bivalent TSS/Enh	Brain Cingulate Gyrus	brain
22	chr12:49364600-49366000	Bivalent Enhancer	Thymus	Thymus
23	chr12:49364800-49365600	Bivalent/Poised TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
24	chr12:49364800-49365600	Bivalent/Poised TSS	Colon Smooth Muscle	Colon
25	chr12:49364800-49365800	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
26	chr12:49364800-49365800	Flanking Bivalent TSS/Enh	ES-UCSF4 Cell Line	embryonic stem cell
27	chr12:49364800-49365800	Flanking Bivalent TSS/Enh	Rectal Mucosa Donor 31	rectum
28	chr12:49364800-49365800	Bivalent/Poised TSS	Rectal Smooth Muscle	rectum
29	chr12:49364800-49365800	Flanking Bivalent TSS/Enh	Dnd41	blood
30	chr12:49364800-49365800	Flanking Active TSS	HMEC	breast
31	chr12:49364800-49366000	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr12:49364800-49366000	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr12:49364800-49366000	Flanking Bivalent TSS/Enh	Duodenum Mucosa	Duodenum
34	chr12:49364800-49366000	Flanking Bivalent TSS/Enh	Fetal Brain Female	brain
35	chr12:49364800-49366000	Flanking Bivalent TSS/Enh	Stomach Smooth Muscle	stomach
36	chr12:49364800-49366800	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr12:49365000-49365600	Bivalent Enhancer	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr12:49365000-49365600	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells	blood
39	chr12:49365000-49365600	Flanking Bivalent TSS/Enh	Fetal Thymus	thymus
40	chr12:49365000-49365600	Flanking Bivalent TSS/Enh	GM12878-XiMat	blood
41	chr12:49365000-49365600	Bivalent Enhancer	HUVEC	blood vessel
42	chr12:49365000-49365600	Flanking Bivalent TSS/Enh	NH-A	brain
43	chr12:49365000-49365800	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell
44	chr12:49365000-49365800	Bivalent Enhancer	Primary T killer memory cells from peripheral blood	blood
45	chr12:49365000-49365800	Flanking Bivalent TSS/Enh	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr12:49365000-49365800	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr12:49365000-49365800	Bivalent/Poised TSS	Brain Dorsolateral Prefrontal Cortex	brain
48	chr12:49365000-49365800	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
49	chr12:49365000-49365800	Bivalent Enhancer	Sigmoid Colon	Sigmoid Colon
50	chr12:49365000-49365800	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood

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