Variant report

Variant	rs1886538
Chromosome Location	chr13:52569963-52569964
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr13:52567202..52571172-chr13:52583807..52586943,6	K562	blood:
2	chr13:52568982..52573456-chr13:52591589..52596221,4	K562	blood:
3	chr13:52566849..52570695-chr13:52572398..52574312,4	K562	blood:
4	chr13:52496511..52499468-chr13:52568718..52570837,2	MCF-7	breast:
5	chr13:52561953..52567975-chr13:52568159..52572243,8	K562	blood:
6	chr13:52564916..52570042-chr13:52571727..52575592,5	MCF-7	breast:
7	chr13:52565945..52573624-chr13:52584322..52588378,8	K562	blood:
8	chr13:52562562..52567113-chr13:52569338..52572980,4	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000253710	Chromatin interaction
ENSG00000123191	Chromatin interaction

Extended variants
information (count: 127 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:116)

rs_ID	r²[population]
rs1004576	0.96[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];0.90[JPT][hapmap];0.86[MEX][hapmap];0.85[TSI][hapmap]
rs1055062	0.87[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1060631	0.88[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11620583	0.95[CHB][hapmap];0.80[CHD][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs12146904	0.91[CHB][hapmap];0.95[CHD][hapmap];0.90[JPT][hapmap]
rs12431310	0.91[CHB][hapmap];0.85[JPT][hapmap]
rs1571189	0.91[CHB][hapmap];0.86[JPT][hapmap]
rs1801243	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs1886542	0.81[CHB][hapmap]
rs1886543	0.91[CHB][hapmap];0.95[CHD][hapmap];0.90[JPT][hapmap]
rs1886544	0.91[CHB][hapmap];0.90[JPT][hapmap]
rs1886547	0.81[CHB][hapmap]
rs1924611	0.95[CHB][hapmap];0.85[JPT][hapmap];0.81[ASN][1000 genomes]
rs2004866	0.81[CHB][hapmap];0.81[JPT][hapmap]
rs2005182	0.80[ASN][1000 genomes]
rs2147359	0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2147360	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2147361	0.96[ASN][1000 genomes]
rs2147363	1.00[ASW][hapmap];0.88[CEU][hapmap];0.90[LWK][hapmap];0.85[TSI][hapmap];0.82[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs2181891	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs2274202	0.81[CHB][hapmap]
rs2277448	0.91[CHB][hapmap];0.90[JPT][hapmap];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2296347	0.91[CHB][hapmap];0.95[CHD][hapmap];0.90[JPT][hapmap]
rs2296348	0.81[CHB][hapmap]
rs2296349	0.81[CHB][hapmap]
rs2408544	0.81[CHB][hapmap]
rs2408546	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2408547	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2408548	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2408550	0.81[CHB][hapmap]
rs2408551	0.81[CHB][hapmap]
rs2408552	0.91[CHB][hapmap];0.93[CHD][hapmap];0.86[JPT][hapmap];0.82[MEX][hapmap]
rs2408554	0.96[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];0.90[JPT][hapmap];0.91[MEX][hapmap];0.85[TSI][hapmap]
rs2408609	0.81[CHB][hapmap]
rs2408611	0.81[CHB][hapmap]
rs2897964	0.87[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];0.90[JPT][hapmap];0.82[MEX][hapmap];0.91[TSI][hapmap];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2897977	0.81[CHB][hapmap]
rs3368	0.81[CHB][hapmap]
rs3742289	0.88[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];0.90[JPT][hapmap];0.86[MEX][hapmap];0.91[TSI][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3742291	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3783240	0.91[CEU][hapmap];0.80[GIH][hapmap];0.95[MEX][hapmap];0.82[TSI][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3783242	0.91[CHB][hapmap];0.95[CHD][hapmap];0.90[JPT][hapmap]
rs3818422	0.91[CHB][hapmap];0.95[CHD][hapmap];0.90[JPT][hapmap]
rs4261421	0.82[ASN][1000 genomes]
rs4264295	0.83[ASN][1000 genomes]
rs4297592	0.81[CHB][hapmap]
rs4497567	0.88[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];0.90[JPT][hapmap];0.82[TSI][hapmap]
rs4600369	0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4941720	0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4941723	0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4941727	0.91[CHB][hapmap];0.90[CHD][hapmap];0.86[JPT][hapmap]
rs61958804	0.86[ASN][1000 genomes]
rs6561656	0.88[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];0.90[JPT][hapmap];0.86[MEX][hapmap];0.91[TSI][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6650384	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6650385	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7318287	0.83[ASN][1000 genomes]
rs7319784	0.91[ASN][1000 genomes]
rs7320252	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7320429	0.84[ASN][1000 genomes]
rs732071	0.88[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.97[TSI][hapmap];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7320831	0.88[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];0.90[JPT][hapmap];0.91[TSI][hapmap];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7321120	0.91[CHB][hapmap];0.95[CHD][hapmap];0.84[GIH][hapmap];0.90[JPT][hapmap];0.86[MEX][hapmap];0.91[ASN][1000 genomes]
rs7321310	0.91[ASN][1000 genomes]
rs7321435	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7321775	0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7324458	0.91[CHB][hapmap];0.95[CHD][hapmap];0.90[JPT][hapmap]
rs7327634	0.81[CHB][hapmap]
rs7332272	0.94[ASN][1000 genomes]
rs7338131	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs747781	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs755363	0.81[CHB][hapmap]
rs7981904	0.91[CHB][hapmap];0.86[JPT][hapmap]
rs7991237	0.81[CHB][hapmap]
rs7994928	0.81[ASN][1000 genomes]
rs7995946	0.81[CHB][hapmap]
rs7998770	0.96[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];0.90[JPT][hapmap];0.91[MEX][hapmap];0.85[TSI][hapmap]
rs9316563	0.95[CHB][hapmap];0.86[JPT][hapmap];0.80[ASN][1000 genomes]
rs9526817	0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9526819	0.95[CHB][hapmap];0.80[CHD][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs9526823	0.88[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];0.90[JPT][hapmap];0.86[MEX][hapmap];0.91[TSI][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9526825	0.88[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];0.90[JPT][hapmap];0.82[TSI][hapmap];0.87[ASN][1000 genomes]
rs9526826	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9526834	0.82[ASN][1000 genomes]
rs9526837	0.81[CHB][hapmap]
rs9526841	0.91[CHB][hapmap];0.90[JPT][hapmap]
rs9535812	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs9535813	0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9535816	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9535819	0.81[ASN][1000 genomes]
rs9535821	0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9535822	0.95[CHB][hapmap];0.80[CHD][hapmap];0.85[JPT][hapmap];0.82[ASN][1000 genomes]
rs9535823	0.81[ASN][1000 genomes]
rs9535824	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9535825	1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs9535826	0.95[CHB][hapmap];0.80[CHD][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs9535832	0.81[CHB][hapmap];0.86[JPT][hapmap]
rs9535836	0.81[CHB][hapmap]
rs9535845	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9535851	0.81[CHB][hapmap]
rs9535856	0.81[CHB][hapmap]
rs9535858	0.81[CHB][hapmap]
rs9535861	0.82[CHB][hapmap];0.81[CHD][hapmap];0.82[MEX][hapmap]
rs9535862	0.81[CHB][hapmap]
rs9535866	0.81[CHB][hapmap]
rs9535867	0.88[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];0.90[JPT][hapmap];0.86[MEX][hapmap];0.85[TSI][hapmap]
rs9535873	0.96[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];0.90[JPT][hapmap];0.86[MEX][hapmap];0.85[TSI][hapmap]
rs9535878	0.81[CHB][hapmap]
rs9535879	0.80[CHB][hapmap]
rs9535880	0.81[CHB][hapmap]
rs9535882	0.81[CHB][hapmap]
rs9535887	0.81[CHB][hapmap]
rs9563089	0.81[CHB][hapmap]
rs9568682	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9568684	0.82[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9568692	0.84[ASN][1000 genomes]
rs9568713	0.81[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:11 , 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
7	nsv1041996	chr13:52544805-52581501	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	n/a
8	esv2763022	chr13:52544978-52581513	Enhancers Weak transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	n/a
9	nsv900082	chr13:52555288-52709938	ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
10	nsv1040931	chr13:52564792-53350914	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
11	nsv541773	chr13:52564792-53350914	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1886538	NEK5	cis	cerebellum	SCAN
rs1886538	CKAP2	cis	parietal	SCAN
rs1886538	LOC440138	cis	multi-tissue	Pritchard
rs1886538	NCRNA00282	cis	cerebellum	SCAN

Chromatin state (count:70 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:52555800-52570200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr13:52567400-52571200	Genic enhancers	HepG2	liver
3	chr13:52568600-52570800	Enhancers	Primary hematopoietic stem cells	blood
4	chr13:52568800-52570200	Bivalent Enhancer	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr13:52568800-52570200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr13:52568800-52570400	Enhancers	Primary monocytes fromperipheralblood	blood
7	chr13:52568800-52570800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr13:52568800-52571200	Enhancers	Cortex derived primary cultured neurospheres	brain
9	chr13:52569200-52570000	Enhancers	Skeletal Muscle Female	skeletal muscle
10	chr13:52569200-52570600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr13:52569200-52570800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr13:52569200-52570800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr13:52569200-52570800	Enhancers	Brain Anterior Caudate	brain
14	chr13:52569200-52570800	Enhancers	Rectal Mucosa Donor 31	rectum
15	chr13:52569200-52570800	Enhancers	Right Atrium	heart
16	chr13:52569200-52571000	Enhancers	Left Ventricle	heart
17	chr13:52569200-52571000	Enhancers	Right Ventricle	heart
18	chr13:52569200-52571200	Enhancers	Fetal Lung	lung
19	chr13:52569200-52571200	Flanking Active TSS	K562	blood
20	chr13:52569200-52572000	Genic enhancers	Fetal Intestine Small	intestine
21	chr13:52569200-52575600	Enhancers	Stomach Mucosa	stomach
22	chr13:52569400-52570200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr13:52569400-52570600	Enhancers	Brain Cingulate Gyrus	brain
24	chr13:52569400-52570800	Enhancers	Brain Hippocampus Middle	brain
25	chr13:52569400-52570800	Enhancers	Colonic Mucosa	Colon
26	chr13:52569400-52570800	Enhancers	Skeletal Muscle Male	skeletal muscle
27	chr13:52569400-52570800	Flanking Active TSS	Stomach Smooth Muscle	stomach
28	chr13:52569400-52571000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr13:52569400-52571000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr13:52569400-52571000	Enhancers	Brain Inferior Temporal Lobe	brain
31	chr13:52569400-52571000	Enhancers	Esophagus	oesophagus
32	chr13:52569400-52571000	Enhancers	Lung	lung
33	chr13:52569400-52571000	Enhancers	Pancreas	Pancrea
34	chr13:52569400-52571000	Enhancers	Psoas Muscle	Psoas
35	chr13:52569400-52571000	Enhancers	Sigmoid Colon	Sigmoid Colon
36	chr13:52569400-52571200	Enhancers	HUES6 Cell Line	embryonic stem cell
37	chr13:52569400-52571200	Enhancers	Fetal Muscle Trunk	muscle
38	chr13:52569400-52571200	Enhancers	Gastric	stomach
39	chr13:52569400-52574400	Enhancers	Placenta	Placenta
40	chr13:52569400-52574600	Enhancers	Fetal Heart	heart
41	chr13:52569400-52575000	Enhancers	Fetal Muscle Leg	muscle
42	chr13:52569400-52575800	Enhancers	Fetal Intestine Large	intestine
43	chr13:52569600-52570000	Flanking Active TSS	Adipose Nuclei	Adipose
44	chr13:52569600-52570000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
45	chr13:52569600-52570000	Flanking Active TSS	Duodenum Mucosa	Duodenum
46	chr13:52569600-52570200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
47	chr13:52569600-52570200	Flanking Active TSS	Rectal Smooth Muscle	rectum
48	chr13:52569600-52570200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
49	chr13:52569600-52570600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
50	chr13:52569600-52570600	Enhancers	Placenta Amnion	Placenta Amnion

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links