Variant report

Variant	rs2057259
Chromosome Location	chr20:13567570-13567571
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 57 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs1040756	0.85[JPT][hapmap];0.82[ASN][1000 genomes]
rs13040087	0.89[ASN][1000 genomes]
rs2057258	0.82[JPT][hapmap];0.89[MKK][hapmap]
rs2070334	0.89[LWK][hapmap];0.94[MKK][hapmap];0.89[YRI][hapmap]
rs2180569	0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2295503	0.90[ASN][1000 genomes]
rs2295504	0.90[CHB][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs2327793	0.86[ASN][1000 genomes]
rs2423732	0.85[ASN][1000 genomes]
rs2423733	0.92[ASN][1000 genomes]
rs2423734	0.86[ASN][1000 genomes]
rs2423737	0.83[ASN][1000 genomes]
rs2423738	0.81[ASN][1000 genomes]
rs2423739	0.85[ASN][1000 genomes]
rs34146992	0.94[ASN][1000 genomes]
rs3789347	0.89[YRI][hapmap]
rs4441543	0.84[ASN][1000 genomes]
rs6033766	0.95[ASN][1000 genomes]
rs6033767	0.92[ASN][1000 genomes]
rs6033768	1.00[ASW][hapmap];0.90[CHB][hapmap];0.91[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.86[MEX][hapmap];0.83[YRI][hapmap];0.95[ASN][1000 genomes]
rs6033783	0.90[ASN][1000 genomes]
rs6033795	0.84[ASN][1000 genomes]
rs6042106	0.89[LWK][hapmap];0.93[MKK][hapmap];0.89[YRI][hapmap]
rs6042128	0.82[JPT][hapmap];0.92[YRI][hapmap]
rs6042224	0.83[YRI][hapmap]
rs6042225	0.95[CHB][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs6042236	1.00[ASW][hapmap];0.90[CHB][hapmap];0.91[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.81[LWK][hapmap];0.83[MEX][hapmap];0.95[ASN][1000 genomes]
rs6042239	0.90[CHB][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs6042240	0.90[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs6042262	0.91[LWK][hapmap]
rs6042264	0.88[ASN][1000 genomes]
rs6042273	0.87[ASN][1000 genomes]
rs6042285	0.81[ASN][1000 genomes]
rs6079074	0.82[JPT][hapmap];0.89[YRI][hapmap]
rs6079095	0.81[JPT][hapmap]
rs6105137	0.92[ASN][1000 genomes]
rs6109983	0.90[CHB][hapmap];0.88[CHD][hapmap];0.90[JPT][hapmap];0.92[ASN][1000 genomes]
rs6109990	0.83[ASN][1000 genomes]
rs6109993	0.83[ASN][1000 genomes]
rs6109995	0.81[ASN][1000 genomes]
rs6131499	0.83[ASN][1000 genomes]
rs6134919	0.94[ASW][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.88[MEX][hapmap];1.00[MKK][hapmap];0.93[YRI][hapmap];0.98[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs6134930	1.00[ASW][hapmap];0.90[CHB][hapmap];0.91[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.83[LWK][hapmap];0.82[MEX][hapmap];0.95[ASN][1000 genomes]
rs6134935	0.95[ASN][1000 genomes]
rs6134948	0.91[ASN][1000 genomes]
rs6514418	0.95[CHB][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]

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	nsv1061303	chr20:13395546-13810990	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv585435	chr20:13410638-13582476	Weak transcription Strong transcription ZNF genes & repeats Enhancers Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	nsv916202	chr20:13421724-14043615	Flanking Active TSS Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
4	nsv1059817	chr20:13422602-13807968	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv458871	chr20:13447896-13573415	Strong transcription Weak transcription ZNF genes & repeats Enhancers Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	nsv585436	chr20:13447896-13573415	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	nsv1066810	chr20:13451869-14432454	Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
8	nsv912687	chr20:13507057-13591596	Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Enhancers Active TSS Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
9	esv1797514	chr20:13541011-13610424	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
10	nsv912688	chr20:13546903-13589682	ZNF genes & repeats Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
11	nsv1061323	chr20:13551004-13746346	Strong transcription ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2057259	MKKS	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:13515000-13605600	Weak transcription	Primary T helper cells PMA-I stimulated	--
2	chr20:13526800-13613800	Weak transcription	Hela-S3	cervix
3	chr20:13535600-13608000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr20:13538200-13571800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
5	chr20:13541200-13578000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr20:13546200-13594200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr20:13546800-13574000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr20:13548000-13568600	Weak transcription	Brain Angular Gyrus	brain
9	chr20:13548600-13568800	Weak transcription	Skeletal Muscle Female	skeletal muscle
10	chr20:13548600-13584600	Weak transcription	Gastric	stomach
11	chr20:13554000-13568400	Weak transcription	Fetal Brain Male	brain
12	chr20:13554600-13577400	Weak transcription	Monocytes-CD14+_RO01746	blood
13	chr20:13556200-13618800	Weak transcription	Skeletal Muscle Male	skeletal muscle
14	chr20:13556600-13567800	Weak transcription	Liver	Liver
15	chr20:13563400-13571200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr20:13563800-13568400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
17	chr20:13563800-13619000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr20:13564000-13567800	Weak transcription	Fetal Muscle Leg	muscle
19	chr20:13564000-13567800	Weak transcription	Left Ventricle	heart
20	chr20:13564000-13569000	Weak transcription	NH-A	brain
21	chr20:13564000-13574000	Weak transcription	Esophagus	oesophagus
22	chr20:13564000-13575000	Weak transcription	Spleen	Spleen
23	chr20:13564000-13583400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr20:13564000-13602600	Weak transcription	Ovary	ovary
25	chr20:13564000-13612400	Weak transcription	Pancreas	Pancrea
26	chr20:13564200-13567800	Weak transcription	Fetal Intestine Large	intestine
27	chr20:13564200-13567800	Weak transcription	HepG2	liver
28	chr20:13564200-13574000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr20:13564200-13583200	Weak transcription	Aorta	Aorta
30	chr20:13564200-13591000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr20:13564200-13592400	Weak transcription	Cortex derived primary cultured neurospheres	brain
32	chr20:13564200-13602400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
33	chr20:13564200-13602800	Weak transcription	Rectal Mucosa Donor 31	rectum
34	chr20:13564200-13608400	Weak transcription	HSMM	muscle
35	chr20:13564400-13567800	Weak transcription	Pancreatic Islets	Pancreatic Islet
36	chr20:13564400-13584400	Weak transcription	Rectal Mucosa Donor 29	rectum
37	chr20:13564800-13573800	Weak transcription	Fetal Stomach	stomach
38	chr20:13566000-13568000	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
39	chr20:13566200-13568000	ZNF genes & repeats	Primary T cells from cord blood	blood
40	chr20:13566400-13567600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr20:13566400-13568000	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
42	chr20:13566400-13569800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr20:13566600-13568200	Weak transcription	Brain Hippocampus Middle	brain
44	chr20:13566600-13568400	Weak transcription	Fetal Heart	heart
45	chr20:13566600-13572600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
46	chr20:13566800-13568000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
47	chr20:13566800-13568200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr20:13566800-13568200	Strong transcription	Fetal Thymus	thymus
49	chr20:13566800-13568400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
50	chr20:13566800-13574200	Weak transcription	H1 Cell Line	embryonic stem cell

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