Variant report

Variant	rs12517724
Chromosome Location	chr5:68627591-68627592
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:22)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:22 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr5:68627479-68628844	HepG2	liver:	n/a	n/a
2	SPI1	chr5:68627292-68627746	HL-60	blood:	n/a	chr5:68627495-68627504 chr5:68627493-68627506
3	TEAD4	chr5:68627428-68627676	H1-hESC	embryonic stem cell:	n/a	n/a
4	CTCF	chr5:68627480-68627630	MCF-7	breast:	n/a	n/a
5	MYBL2	chr5:68627533-68628258	HepG2	liver:	n/a	n/a
6	HEY1	chr5:68627514-68627724	HepG2	liver:	n/a	n/a
7	SMC3	chr5:68627545-68628044	HepG2	liver:	n/a	n/a
8	HEY1	chr5:68627333-68628141	HepG2	liver:	n/a	n/a
9	POLR2A	chr5:68627443-68627689	HepG2	liver:	n/a	n/a
10	TBP	chr5:68627466-68628129	HepG2	liver:	n/a	n/a
11	POLR2A	chr5:68627471-68627591	MCF-7	breast:	n/a	n/a
12	BHLHE40	chr5:68627456-68627662	K562	blood:	n/a	n/a
13	ZNF263	chr5:68627408-68627907	HEK293-T-REx	kidney:	n/a	chr5:68627520-68627529
14	POLR2A	chr5:68627305-68628118	HepG2	liver:	n/a	n/a
15	MXI1	chr5:68627542-68628106	HepG2	liver:	n/a	n/a
16	ELF1	chr5:68627366-68627919	HepG2	liver:	n/a	n/a
17	MYBL2	chr5:68627423-68628186	HepG2	liver:	n/a	n/a
18	TEAD4	chr5:68627399-68628231	HepG2	liver:	n/a	n/a
19	POLR2A	chr5:68627441-68628937	HepG2	liver:	n/a	n/a
20	POLR2A	chr5:68626982-68628073	MCF-7	breast:	n/a	n/a
21	STAT3	chr5:68627538-68627616	MCF10A-Er-Src	breast:	n/a	n/a
22	POLR2A	chr5:68627487-68627761	HepG2	liver:	n/a	n/a

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr5:68626792..68633026-chr5:68660168..68667090,13	MCF-7	breast:
2	chr5:68626762..68628383-chr5:68787111..68789288,2	MCF-7	breast:
3	chr5:68485299..68487066-chr5:68626120..68629033,4	MCF-7	breast:
4	chr5:68626462..68633259-chr5:68656360..68665608,14	MCF-7	breast:
5	chr5:68606839..68610803-chr5:68625940..68628885,4	MCF-7	breast:
6	chr5:68529975..68532202-chr5:68627120..68629377,3	MCF-7	breast:
7	chr5:68588146..68590724-chr5:68626782..68628489,2	MCF-7	breast:
8	chr5:68626208..68627882-chr5:68665634..68668081,2	MCF-7	breast:
9	chr5:68511595..68514121-chr5:68626401..68628217,2	MCF-7	breast:
10	chr5:68534808..68537076-chr5:68626446..68628069,2	MCF-7	breast:
11	chr5:68388706..68391393-chr5:68627238..68631529,6	MCF-7	breast:

No data

Variant related genes	Relation type
CHCHD2P2	TF binding region
ENSG00000153044	Chromatin interaction
ENSG00000145740	Chromatin interaction
ENSG00000134058	Chromatin interaction
ENSG00000213830	Chromatin interaction
ENSG00000134056	Chromatin interaction
ENSG00000152942	Chromatin interaction
ENSG00000085231	Chromatin interaction
ENSG00000197822	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10044508	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10045361	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10471350	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10471774	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10471775	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10471776	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10940212	0.83[EUR][1000 genomes]
rs10940216	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10940218	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11748974	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12187268	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12188076	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13178839	0.81[EUR][1000 genomes]
rs13361598	0.82[EUR][1000 genomes]
rs1530290	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2010352	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs28580747	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34935424	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4252228	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4473723	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4976160	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4976189	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4976190	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4976194	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs58772585	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62373187	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6450029	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6450032	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6873869	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6875069	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6879078	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7708429	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7712318	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9291947	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9291948	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9791036	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1018151	chr5:68377118-68667581	Enhancers Active TSS Flanking Active TSS Genic enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
2	nsv1035004	chr5:68405526-68670101	Strong transcription Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
3	nsv969960	chr5:68613678-68646127	Active TSS Flanking Active TSS Weak transcription Strong transcription Enhancers Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
4	esv3515528	chr5:68624487-68653938	Strong transcription Flanking Active TSS Weak transcription Active TSS Enhancers Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
5	esv3515529	chr5:68624487-68653938	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
6	nsv881767	chr5:68625786-68733698	Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12517724	MRPS36	Cis_1M	lymphoblastoid	RTeQTL
rs12517724	CCDC125	cis	lung	GTEx

Chromatin state (count:78 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:68576400-68627600	Weak transcription	Brain Substantia Nigra	brain
2	chr5:68576400-68627800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
3	chr5:68576600-68627800	Weak transcription	Brain Angular Gyrus	brain
4	chr5:68577400-68628200	Weak transcription	Small Intestine	intestine
5	chr5:68581600-68627600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr5:68581800-68627600	Weak transcription	Brain Anterior Caudate	brain
7	chr5:68591600-68627600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr5:68599600-68627800	Weak transcription	NH-A	brain
9	chr5:68601400-68627600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
10	chr5:68609600-68627600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr5:68609800-68627600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
12	chr5:68609800-68627600	Weak transcription	Fetal Thymus	thymus
13	chr5:68609800-68628200	Weak transcription	Right Ventricle	heart
14	chr5:68609800-68628400	Weak transcription	Lung	lung
15	chr5:68610400-68627600	Weak transcription	Primary B cells from peripheral blood	blood
16	chr5:68610600-68627800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
17	chr5:68611000-68628200	Weak transcription	Aorta	Aorta
18	chr5:68616600-68628200	Weak transcription	Left Ventricle	heart
19	chr5:68617000-68627600	Weak transcription	Duodenum Smooth Muscle	Duodenum
20	chr5:68621000-68628200	Weak transcription	Sigmoid Colon	Sigmoid Colon
21	chr5:68621400-68627600	Weak transcription	Primary T cells from cord blood	blood
22	chr5:68622800-68627600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr5:68626400-68627600	Enhancers	Stomach Mucosa	stomach
24	chr5:68626600-68627600	Enhancers	A549	lung
25	chr5:68626800-68627800	Enhancers	Skeletal Muscle Male	skeletal muscle
26	chr5:68627000-68627600	Active TSS	Placenta	Placenta
27	chr5:68627000-68627800	Weak transcription	Fetal Brain Female	brain
28	chr5:68627000-68628800	Active TSS	Duodenum Mucosa	Duodenum
29	chr5:68627200-68627600	Enhancers	Breast Myoepithelial Primary Cells	Breast
30	chr5:68627200-68627600	Enhancers	Primary hematopoietic stem cells	blood
31	chr5:68627200-68627600	Flanking Active TSS	Fetal Intestine Large	intestine
32	chr5:68627200-68627800	Flanking Active TSS	Liver	Liver
33	chr5:68627200-68627800	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
34	chr5:68627200-68627800	Flanking Active TSS	HepG2	liver
35	chr5:68627200-68628000	Active TSS	Rectal Smooth Muscle	rectum
36	chr5:68627200-68628400	Weak transcription	Gastric	stomach
37	chr5:68627200-68628800	Active TSS	Colonic Mucosa	Colon
38	chr5:68627200-68629200	Active TSS	Rectal Mucosa Donor 29	rectum
39	chr5:68627400-68627600	Enhancers	HUES64 Cell Line	embryonic stem cell
40	chr5:68627400-68627600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr5:68627400-68627600	Enhancers	Primary T helper cells PMA-I stimulated	--
42	chr5:68627400-68627600	Enhancers	Primary T helper cells fromperipheralblood	blood
43	chr5:68627400-68627600	Enhancers	Primary T killer memory cells from peripheral blood	blood
44	chr5:68627400-68627600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr5:68627400-68627600	Enhancers	Esophagus	oesophagus
46	chr5:68627400-68627600	Enhancers	Fetal Muscle Trunk	muscle
47	chr5:68627400-68627600	Enhancers	Pancreas	Pancrea
48	chr5:68627400-68627600	Enhancers	Skeletal Muscle Female	skeletal muscle
49	chr5:68627400-68627600	Enhancers	Dnd41	blood
50	chr5:68627400-68627600	Enhancers	GM12878-XiMat	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links