Variant report

Variant	rs372370
Chromosome Location	chr5:52903922-52903923
allele	A/G
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	TCF7L2	chr5:52903861-52904058	PANC-1	pancreas:	n/a	n/a
2	FOS	chr5:52903878-52903968	MCF10A-Er-Src	breast:	n/a	n/a

Variant related genes	Relation type
ENSG00000238508	TF binding region

Extended variants
information (count: 104 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:94)

rs_ID	r²[population]
rs10036570	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10471866	0.86[ASN][1000 genomes]
rs10940328	0.84[ASN][1000 genomes]
rs12514280	0.82[ASN][1000 genomes]
rs12654088	0.84[ASN][1000 genomes]
rs13164833	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13179304	0.86[ASN][1000 genomes]
rs1490769	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs171740	0.85[ASN][1000 genomes]
rs1844697	0.89[ASN][1000 genomes]
rs1873426	0.87[ASN][1000 genomes]
rs187658	0.86[ASN][1000 genomes]
rs189848	0.85[ASN][1000 genomes]
rs189849	0.87[ASN][1000 genomes]
rs194364	0.87[ASN][1000 genomes]
rs256081	0.87[ASN][1000 genomes]
rs256082	0.88[ASN][1000 genomes]
rs256086	0.89[ASN][1000 genomes]
rs256092	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs256093	0.87[ASN][1000 genomes]
rs256094	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs256096	0.85[ASN][1000 genomes]
rs256098	0.87[ASN][1000 genomes]
rs256099	0.87[ASN][1000 genomes]
rs256109	0.86[ASN][1000 genomes]
rs256111	0.86[ASN][1000 genomes]
rs256114	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs256115	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs256118	0.91[ASN][1000 genomes]
rs256119	0.89[ASN][1000 genomes]
rs2607476	0.89[ASN][1000 genomes]
rs2607477	0.91[ASN][1000 genomes]
rs2607478	0.91[ASN][1000 genomes]
rs2607482	0.81[ASN][1000 genomes]
rs2607483	0.87[ASN][1000 genomes]
rs2607485	0.87[ASN][1000 genomes]
rs2607503	0.87[ASN][1000 genomes]
rs2607506	0.87[ASN][1000 genomes]
rs2607508	0.89[ASN][1000 genomes]
rs2607510	0.89[ASN][1000 genomes]
rs2636993	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2637002	0.87[ASN][1000 genomes]
rs2637026	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2637029	0.85[ASN][1000 genomes]
rs2655381	0.82[ASN][1000 genomes]
rs3103597	0.89[ASN][1000 genomes]
rs3103598	0.89[ASN][1000 genomes]
rs3103601	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3103602	0.88[ASN][1000 genomes]
rs31308	0.87[ASN][1000 genomes]
rs34071992	0.85[ASN][1000 genomes]
rs365358	0.89[ASN][1000 genomes]
rs365578	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs365932	0.89[ASN][1000 genomes]
rs366313	0.89[ASN][1000 genomes]
rs368461	0.89[ASN][1000 genomes]
rs372215	0.89[ASN][1000 genomes]
rs377077	0.91[ASN][1000 genomes]
rs377159	0.89[ASN][1000 genomes]
rs381575	0.88[ASN][1000 genomes]
rs388311	0.87[ASN][1000 genomes]
rs392169	0.89[ASN][1000 genomes]
rs401967	0.87[ASN][1000 genomes]
rs402751	0.89[ASN][1000 genomes]
rs404838	0.89[ASN][1000 genomes]
rs409313	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs412559	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs417550	0.89[ASN][1000 genomes]
rs425085	0.86[ASN][1000 genomes]
rs42565	0.89[ASN][1000 genomes]
rs425880	0.89[ASN][1000 genomes]
rs426196	0.86[ASN][1000 genomes]
rs427527	0.90[AFR][1000 genomes]
rs432020	0.91[ASN][1000 genomes]
rs435713	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs438736	0.91[ASN][1000 genomes]
rs443254	0.91[ASN][1000 genomes]
rs444848	0.86[ASN][1000 genomes]
rs445347	0.87[ASN][1000 genomes]
rs449208	0.89[ASN][1000 genomes]
rs451591	0.89[ASN][1000 genomes]
rs451881	0.89[ASN][1000 genomes]
rs454735	0.89[ASN][1000 genomes]
rs499760	0.89[ASN][1000 genomes]
rs524289	0.86[ASN][1000 genomes]
rs535277	0.87[ASN][1000 genomes]
rs6864497	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs693204	0.89[ASN][1000 genomes]
rs7717681	0.86[ASN][1000 genomes]
rs786330	0.86[ASN][1000 genomes]
rs786331	0.86[ASN][1000 genomes]
rs786334	0.90[ASN][1000 genomes]
rs9292024	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9687844	0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2752745	chr5:52422063-53343529	Transcr. at gene 5' and 3' ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	nsv1032632	chr5:52667145-53655624	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv880868	chr5:52799618-53002783	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv880689	chr5:52847995-53002783	ZNF genes & repeats Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv881348	chr5:52885100-52942083	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
6	nsv881237	chr5:52885100-52944428	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
7	nsv880426	chr5:52885100-52953048	Weak transcription Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
8	nsv881604	chr5:52885100-53035301	Weak transcription Genic enhancers Enhancers Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
9	nsv880762	chr5:52894276-52944428	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
10	nsv4828	chr5:52895470-52940279	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:52860000-52909000	Weak transcription	Small Intestine	intestine
2	chr5:52876800-52907400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr5:52885800-52906000	Weak transcription	Psoas Muscle	Psoas
4	chr5:52888000-52905000	Weak transcription	Right Ventricle	heart
5	chr5:52888800-52908200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
6	chr5:52889000-52904200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
7	chr5:52889800-52920800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr5:52890000-52912400	Weak transcription	K562	blood
9	chr5:52890200-52907200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
10	chr5:52890200-52920000	Weak transcription	HepG2	liver
11	chr5:52894200-52905600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr5:52897800-52904000	Weak transcription	NH-A	brain
13	chr5:52897800-52904200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr5:52897800-52906200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr5:52898800-52904200	Weak transcription	Thymus	Thymus
16	chr5:52899000-52904200	Weak transcription	Primary neutrophils fromperipheralblood	blood
17	chr5:52899000-52904600	Strong transcription	Primary B cells from peripheral blood	blood
18	chr5:52899200-52904000	Weak transcription	Brain Cingulate Gyrus	brain
19	chr5:52899200-52904000	Weak transcription	Skeletal Muscle Male	skeletal muscle
20	chr5:52899200-52904400	Strong transcription	HUES64 Cell Line	embryonic stem cell
21	chr5:52899200-52904400	Weak transcription	Colonic Mucosa	Colon
22	chr5:52899200-52904800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr5:52899200-52905800	Weak transcription	Fetal Brain Female	brain
24	chr5:52899200-52906000	Strong transcription	Monocytes-CD14+_RO01746	blood
25	chr5:52899200-52908400	Weak transcription	Rectal Smooth Muscle	rectum
26	chr5:52899200-52908400	Weak transcription	HMEC	breast
27	chr5:52899200-52910200	Weak transcription	Brain Germinal Matrix	brain
28	chr5:52899400-52904000	Weak transcription	Ovary	ovary
29	chr5:52899400-52905600	Weak transcription	NHLF	lung
30	chr5:52899400-52908200	Weak transcription	Colon Smooth Muscle	Colon
31	chr5:52899400-52908200	Weak transcription	Pancreatic Islets	Pancreatic Islet
32	chr5:52899400-52908400	Weak transcription	Cortex derived primary cultured neurospheres	brain
33	chr5:52899400-52908400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr5:52899400-52928400	Weak transcription	Fetal Heart	heart
35	chr5:52899800-52904600	Strong transcription	Adipose Nuclei	Adipose
36	chr5:52899800-52905000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr5:52899800-52905600	Strong transcription	Primary hematopoietic stem cells	blood
38	chr5:52899800-52906400	Strong transcription	Primary monocytes fromperipheralblood	blood
39	chr5:52900000-52906200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
40	chr5:52900200-52904600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr5:52900200-52905000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr5:52900400-52904800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
43	chr5:52900400-52905400	Strong transcription	Primary T cells from cord blood	blood
44	chr5:52900600-52905000	Weak transcription	Hela-S3	cervix
45	chr5:52900800-52904000	Weak transcription	HSMM	muscle
46	chr5:52900800-52905600	Weak transcription	Fetal Kidney	kidney
47	chr5:52900800-52905800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
48	chr5:52900800-52908600	Weak transcription	A549	lung
49	chr5:52900800-52909000	Weak transcription	Esophagus	oesophagus
50	chr5:52900800-52910200	Weak transcription	Primary T helper naive cells from peripheral blood	blood

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