Variant report

Variant	rs59594854
Chromosome Location	chr12:118811805-118811806
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:26)
CpG islands
(count:0)
Chromatin interactive
region (count:15)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:26 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr12:118810453-118811825	HepG2	liver:	n/a	n/a
2	TAL1	chr12:118810572-118811887	K562	blood:	n/a	n/a
3	IRF1	chr12:118810555-118811806	K562	blood:	n/a	chr12:118810748-118810762
4	POLR2A	chr12:118810426-118811812	NB4	blood:	n/a	n/a
5	POLR2A	chr12:118810475-118811863	K562	blood:	n/a	n/a
6	EP300	chr12:118810534-118811892	K562	blood:	n/a	chr12:118810677-118810686 chr12:118810674-118810683
7	IRF1	chr12:118810513-118811870	K562	blood:	n/a	chr12:118810748-118810762
8	MYC	chr12:118810427-118811851	K562	blood:	n/a	n/a
9	POLR2A	chr12:118810219-118811912	K562	blood:	n/a	n/a
10	ARID3A	chr12:118810578-118811876	HepG2	liver:	n/a	n/a
11	NR2F2	chr12:118810651-118811876	K562	blood:	n/a	n/a
12	POLR2A	chr12:118810409-118811891	U87	brain:	n/a	n/a
13	POLR2A	chr12:118810842-118811829	HepG2	liver:	n/a	n/a
14	POLR2A	chr12:118810459-118811820	GM12891	blood:	n/a	n/a
15	POLR2A	chr12:118810505-118811843	K562	blood:	n/a	n/a
16	HCFC1	chr12:118810302-118811953	Hela-S3	cervix:	n/a	n/a
17	POLR2A	chr12:118810466-118811929	MCF10A-Er-Src	breast:	n/a	n/a
18	POLR2A	chr12:118810460-118811863	K562	blood:	n/a	n/a
19	MXI1	chr12:118811654-118811843	GM12878	blood:	n/a	n/a
20	POLR2A	chr12:118810481-118811894	K562	blood:	n/a	n/a
21	MYC	chr12:118810378-118811999	K562	blood:	n/a	chr12:118810404-118810414
22	POLR2A	chr12:118810409-118811872	U87	brain:	n/a	n/a
23	HEY1	chr12:118810826-118811834	HepG2	liver:	n/a	n/a
24	HEY1	chr12:118810445-118811816	HepG2	liver:	n/a	chr12:118810672-118810687
25	POLR2A	chr12:118810306-118812239	HepG2	liver:	n/a	n/a
26	TBP	chr12:118810445-118811837	K562	blood:	n/a	n/a

No data

(count:15 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:118666340..118669274-chr12:118811225..118812911,2	MCF-7	breast:
2	chr12:118751783..118754702-chr12:118810776..118812505,2	K562	blood:
3	chr12:118670146..118671959-chr12:118810899..118813142,2	MCF-7	breast:
4	chr12:118577698..118580180-chr12:118811113..118813216,2	MCF-7	breast:
5	chr12:118674302..118676883-chr12:118810896..118813058,3	MCF-7	breast:
6	chr12:118789693..118801109-chr12:118805205..118813455,21	K562	blood:
7	chr12:118558717..118560861-chr12:118811542..118813614,2	K562	blood:
8	chr12:118601731..118605413-chr12:118811549..118815749,6	MCF-7	breast:
9	chr12:118573102..118576254-chr12:118808901..118815960,7	MCF-7	breast:
10	chr12:118602929..118605254-chr12:118810718..118812251,2	K562	blood:
11	chr12:118604051..118606436-chr12:118810994..118813151,2	MCF-7	breast:
12	chr12:118791019..118798938-chr12:118809011..118813946,9	MCF-7	breast:
13	chr12:118792933..118800473-chr12:118805927..118813309,24	K562	blood:
14	chr12:118612128..118614340-chr12:118811467..118813100,2	MCF-7	breast:
15	chr12:118638724..118640594-chr12:118810784..118812979,2	K562	blood:

No data

Variant related genes	Relation type
SUDS3	TF binding region
TAOK3	TF binding region
ENSG00000221280	Chromatin interaction
ENSG00000089220	Chromatin interaction
ENSG00000176834	Chromatin interaction
ENSG00000135090	Chromatin interaction

Extended variants
information (count: 76 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs10082823	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10850967	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11068910	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11068917	0.88[EUR][1000 genomes]
rs11068919	0.91[EUR][1000 genomes]
rs11068926	0.94[EUR][1000 genomes]
rs12308475	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17440823	0.81[EUR][1000 genomes]
rs17440893	0.85[EUR][1000 genomes]
rs17440942	0.86[EUR][1000 genomes]
rs17512574	0.81[EUR][1000 genomes]
rs17512609	0.82[EUR][1000 genomes]
rs17512644	0.83[EUR][1000 genomes]
rs17512652	0.83[EUR][1000 genomes]
rs17512763	0.86[EUR][1000 genomes]
rs17619932	0.89[EUR][1000 genomes]
rs1909617	0.86[EUR][1000 genomes]
rs2036314	0.95[EUR][1000 genomes]
rs2036489	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2055534	0.86[EUR][1000 genomes]
rs2062519	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4442583	0.94[EUR][1000 genomes]
rs4766899	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4766900	0.87[EUR][1000 genomes]
rs4767669	0.86[EUR][1000 genomes]
rs4767670	0.86[EUR][1000 genomes]
rs4767672	0.86[EUR][1000 genomes]
rs56133316	0.86[EUR][1000 genomes]
rs56157623	0.86[EUR][1000 genomes]
rs56284927	0.81[EUR][1000 genomes]
rs56324376	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61943365	0.82[EUR][1000 genomes]
rs61943367	0.86[EUR][1000 genomes]
rs61943368	0.86[EUR][1000 genomes]
rs61943369	0.95[EUR][1000 genomes]
rs61943370	0.94[EUR][1000 genomes]
rs61943371	0.94[EUR][1000 genomes]
rs61943385	0.86[EUR][1000 genomes]
rs61943388	0.86[EUR][1000 genomes]
rs61943389	0.86[EUR][1000 genomes]
rs61943391	0.85[EUR][1000 genomes]
rs61943392	0.86[EUR][1000 genomes]
rs61943393	0.86[EUR][1000 genomes]
rs61943397	0.87[EUR][1000 genomes]
rs61943399	0.86[EUR][1000 genomes]
rs61943400	0.86[EUR][1000 genomes]
rs61943401	0.86[EUR][1000 genomes]
rs61943402	0.86[EUR][1000 genomes]
rs61943403	0.87[EUR][1000 genomes]
rs61943404	0.86[EUR][1000 genomes]
rs61946063	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6490173	0.80[EUR][1000 genomes]
rs6490175	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6490177	0.93[EUR][1000 genomes]
rs7137055	0.86[EUR][1000 genomes]
rs7137184	0.86[EUR][1000 genomes]
rs7294498	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7295288	0.80[EUR][1000 genomes]
rs7296214	0.85[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs7299040	0.86[EUR][1000 genomes]
rs7304342	0.87[EUR][1000 genomes]
rs7309484	0.86[EUR][1000 genomes]
rs7315458	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73205551	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs73205576	0.86[EUR][1000 genomes]
rs73205594	0.86[EUR][1000 genomes]
rs7957828	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7967900	0.86[EUR][1000 genomes]
rs7968011	0.86[EUR][1000 genomes]
rs7968371	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs884844	0.86[EUR][1000 genomes]
rs950288	0.86[EUR][1000 genomes]
rs9943819	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1053785	chr12:118490955-118874194	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
2	nsv899547	chr12:118791441-118896304	ZNF genes & repeats Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
3	esv3413770	chr12:118808569-118812117	Flanking Active TSS Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs59594854	SUDS3	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:118811000-118812000	Flanking Active TSS	Primary hematopoietic stem cells	blood
2	chr12:118811000-118812000	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
3	chr12:118811000-118812000	Flanking Active TSS	Hela-S3	cervix
4	chr12:118811000-118812200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
5	chr12:118811200-118812000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr12:118811200-118812000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
7	chr12:118811200-118812000	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
8	chr12:118811200-118812000	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
9	chr12:118811200-118812000	Flanking Active TSS	Dnd41	blood
10	chr12:118811200-118812400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr12:118811200-118812400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr12:118811200-118812600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
13	chr12:118811200-118813800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr12:118811200-118813800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr12:118811200-118813800	Weak transcription	Gastric	stomach
16	chr12:118811200-118813800	Weak transcription	Pancreas	Pancrea
17	chr12:118811400-118812000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr12:118811400-118812000	Enhancers	Primary monocytes fromperipheralblood	blood
19	chr12:118811400-118812000	Weak transcription	Right Ventricle	heart
20	chr12:118811400-118812200	Enhancers	Sigmoid Colon	Sigmoid Colon
21	chr12:118811400-118812200	Enhancers	Small Intestine	intestine
22	chr12:118811400-118812400	Flanking Active TSS	K562	blood
23	chr12:118811400-118812600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr12:118811400-118812800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr12:118811400-118813600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
26	chr12:118811400-118813800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr12:118811400-118813800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr12:118811400-118813800	Weak transcription	Aorta	Aorta
29	chr12:118811400-118813800	Weak transcription	Esophagus	oesophagus
30	chr12:118811400-118813800	Weak transcription	Lung	lung
31	chr12:118811600-118812000	Enhancers	Primary B cells from cord blood	blood
32	chr12:118811600-118812000	Enhancers	Primary B cells from peripheral blood	blood
33	chr12:118811600-118812000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
34	chr12:118811600-118812000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
35	chr12:118811600-118812000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
36	chr12:118811600-118812000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
37	chr12:118811600-118812000	Enhancers	Rectal Mucosa Donor 31	rectum
38	chr12:118811600-118812200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr12:118811600-118812200	Enhancers	Primary T helper cells fromperipheralblood	blood
40	chr12:118811600-118812200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
41	chr12:118811600-118812200	Enhancers	Colonic Mucosa	Colon
42	chr12:118811600-118812200	Enhancers	Fetal Intestine Large	intestine
43	chr12:118811600-118812200	Enhancers	Fetal Intestine Small	intestine
44	chr12:118811600-118812400	Enhancers	Primary T cells fromperipheralblood	blood
45	chr12:118811600-118812400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
46	chr12:118811600-118812400	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
47	chr12:118811600-118812400	Enhancers	HSMM	muscle
48	chr12:118811600-118813200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
49	chr12:118811600-118813200	Enhancers	Brain Angular Gyrus	brain
50	chr12:118811600-118813600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin

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