Variant report

Variant	rs61957455
Chromosome Location	chr13:52540786-52540787
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	POLR2A	chr13:52540749-52541085	GM12891	blood:	n/a	n/a
2	POLR2A	chr13:52540595-52541202	H1-hESC	embryonic stem cell:	n/a	n/a
3	POLR2A	chr13:52540605-52541062	GM12892	blood:	n/a	n/a
4	MAFK	chr13:52540590-52540909	HepG2	liver:	n/a	chr13:52540702-52540713
5	MAFK	chr13:52540591-52540860	HepG2	liver:	n/a	chr13:52540702-52540713
6	TAF1	chr13:52540773-52540995	H1-hESC	embryonic stem cell:	n/a	n/a
7	MAFK	chr13:52540678-52540790	K562	blood:	n/a	chr13:52540702-52540713
8	EBF1	chr13:52540763-52541004	GM12878	blood:	n/a	n/a
9	POLR2A	chr13:52540587-52541147	GM12878	blood:	n/a	n/a
10	MAFK	chr13:52540615-52540839	IMR90	lung:	n/a	chr13:52540702-52540713
11	POLR2A	chr13:52540747-52541019	GM12892	blood:	n/a	n/a
12	POLR2A	chr13:52540782-52540977	A549	lung:	n/a	n/a
13	HEY1	chr13:52540761-52541020	HepG2	liver:	n/a	n/a
14	POLR2A	chr13:52540709-52540955	GM12891	blood:	n/a	n/a
15	MAFF	chr13:52540593-52540882	HepG2	liver:	n/a	chr13:52540753-52540771
16	POLR2A	chr13:52540745-52541044	GM12878	blood:	n/a	n/a
17	MAFF	chr13:52540672-52540791	K562	blood:	n/a	chr13:52540753-52540771
18	POLR2A	chr13:52540722-52541172	GM12892	blood:	n/a	n/a

Variant related genes	Relation type
FABP5P2	TF binding region
ATP7B	TF binding region

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs1801247	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60579905	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61957235	1.00[AFR][1000 genomes]
rs61957424	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61957425	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61957447	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61957449	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61957453	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61957454	0.80[EUR][1000 genomes]
rs8002753	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9526807	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9526809	1.00[AFR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9526813	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9535794	1.00[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs9535803	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9535804	1.00[AFR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9535805	1.00[AFR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9535806	1.00[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs9535807	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9535808	1.00[AFR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9535809	0.83[EUR][1000 genomes]
rs9535827	1.00[AFR][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	nsv530718	chr13:52291802-52832752	Enhancers ZNF genes & repeats Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
2	nsv1044310	chr13:52321564-52643924	Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
3	nsv1050117	chr13:52325116-52643924	Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
4	nsv934070	chr13:52362588-53174923	Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Active TSS Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
5	nsv455888	chr13:52491193-52570728	Genic enhancers Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
6	nsv561649	chr13:52491193-52570728	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:52488200-52542200	Weak transcription	Brain Cingulate Gyrus	brain
2	chr13:52494400-52558000	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr13:52501000-52550400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr13:52509200-52549800	Weak transcription	Brain Substantia Nigra	brain
5	chr13:52509200-52553000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr13:52509400-52548600	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr13:52512600-52544000	Weak transcription	Brain Angular Gyrus	brain
8	chr13:52513200-52553000	Weak transcription	Placenta	Placenta
9	chr13:52513400-52542000	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr13:52513400-52555400	Weak transcription	Brain Hippocampus Middle	brain
11	chr13:52516000-52548000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr13:52516600-52554000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr13:52516800-52555400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr13:52519400-52546000	Weak transcription	Spleen	Spleen
15	chr13:52520600-52553000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr13:52525200-52550200	Weak transcription	Fetal Brain Female	brain
17	chr13:52525400-52553000	Weak transcription	Ovary	ovary
18	chr13:52528000-52543200	Weak transcription	Cortex derived primary cultured neurospheres	brain
19	chr13:52528400-52540800	Weak transcription	Lung	lung
20	chr13:52528400-52544000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
21	chr13:52528800-52542200	Weak transcription	Fetal Heart	heart
22	chr13:52529600-52553000	Weak transcription	Psoas Muscle	Psoas
23	chr13:52529800-52541800	Weak transcription	Skeletal Muscle Male	skeletal muscle
24	chr13:52530200-52542000	Weak transcription	Brain Germinal Matrix	brain
25	chr13:52530200-52555400	Weak transcription	Skeletal Muscle Female	skeletal muscle
26	chr13:52530400-52541600	Weak transcription	Fetal Thymus	thymus
27	chr13:52530400-52549000	Weak transcription	Placenta Amnion	Placenta Amnion
28	chr13:52530600-52550400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr13:52530800-52544600	Weak transcription	Pancreas	Pancrea
30	chr13:52530800-52553000	Weak transcription	Fetal Lung	lung
31	chr13:52532400-52541800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr13:52532800-52542000	Weak transcription	Brain Anterior Caudate	brain
33	chr13:52532800-52548200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr13:52532800-52553000	Weak transcription	Fetal Muscle Trunk	muscle
35	chr13:52533200-52544600	Strong transcription	HepG2	liver
36	chr13:52534200-52541600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr13:52534400-52544600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr13:52534400-52555400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
39	chr13:52534600-52542000	Weak transcription	Gastric	stomach
40	chr13:52534600-52546000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
41	chr13:52536200-52548400	Weak transcription	Colonic Mucosa	Colon
42	chr13:52536600-52545000	Weak transcription	Sigmoid Colon	Sigmoid Colon
43	chr13:52537000-52541800	Weak transcription	Stomach Mucosa	stomach
44	chr13:52537000-52542000	Strong transcription	Fetal Intestine Small	intestine
45	chr13:52537000-52552800	Weak transcription	Rectal Mucosa Donor 31	rectum
46	chr13:52537400-52542000	Weak transcription	K562	blood
47	chr13:52538600-52544600	Strong transcription	Liver	Liver
48	chr13:52538800-52541400	Weak transcription	Colon Smooth Muscle	Colon
49	chr13:52539000-52541400	Strong transcription	Fetal Intestine Large	intestine
50	chr13:52539200-52543600	Strong transcription	Fetal Stomach	stomach

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