Variant report

Variant	rs6042239
Chromosome Location	chr20:13583514-13583515
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 60 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs1040756	0.85[CHB][hapmap];0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs11087055	0.82[ASN][1000 genomes]
rs13040087	0.94[ASN][1000 genomes]
rs2057259	0.90[CHB][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs2180569	0.95[CHB][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs2295503	0.95[ASN][1000 genomes]
rs2295504	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2295506	0.87[YRI][hapmap];0.89[AFR][1000 genomes]
rs2327793	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2423732	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2423733	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2423734	0.91[ASN][1000 genomes]
rs2423736	0.84[ASN][1000 genomes]
rs2423737	0.88[ASN][1000 genomes]
rs2423738	0.85[ASN][1000 genomes]
rs2423739	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34146992	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34822601	0.82[ASN][1000 genomes]
rs3789347	0.83[YRI][hapmap]
rs4303776	0.81[ASN][1000 genomes]
rs4441543	0.89[ASN][1000 genomes]
rs6033766	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6033767	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6033768	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6033772	0.96[YRI][hapmap];0.90[AFR][1000 genomes]
rs6033778	0.87[AFR][1000 genomes]
rs6033783	0.95[ASN][1000 genomes]
rs6033795	0.89[ASN][1000 genomes]
rs6042225	1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs6042235	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6042236	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6042240	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6042245	0.96[YRI][hapmap];0.88[AFR][1000 genomes]
rs6042256	0.87[YRI][hapmap];0.89[AFR][1000 genomes]
rs6042264	0.93[ASN][1000 genomes]
rs6042273	0.92[ASN][1000 genomes]
rs6042285	0.86[ASN][1000 genomes]
rs6042301	0.85[CHB][hapmap];0.82[JPT][hapmap];0.82[ASN][1000 genomes]
rs6079074	0.83[YRI][hapmap]
rs6105137	0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6109983	1.00[CHB][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs6109990	0.87[ASN][1000 genomes]
rs6109993	0.88[ASN][1000 genomes]
rs6109995	0.86[ASN][1000 genomes]
rs6131499	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6134919	0.85[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs6134930	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6134935	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6134948	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6514418	1.00[CHB][hapmap];0.91[JPT][hapmap];0.92[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	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	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
3	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
4	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
5	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
6	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
7	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
8	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
9	nsv912689	chr20:13570331-14155881	Weak transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
10	nsv531478	chr20:13580524-13814797	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:66 , 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	chr20:13546200-13594200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr20:13548600-13584600	Weak transcription	Gastric	stomach
6	chr20:13556200-13618800	Weak transcription	Skeletal Muscle Male	skeletal muscle
7	chr20:13563800-13619000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr20:13564000-13602600	Weak transcription	Ovary	ovary
9	chr20:13564000-13612400	Weak transcription	Pancreas	Pancrea
10	chr20:13564200-13591000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr20:13564200-13592400	Weak transcription	Cortex derived primary cultured neurospheres	brain
12	chr20:13564200-13602400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr20:13564200-13602800	Weak transcription	Rectal Mucosa Donor 31	rectum
14	chr20:13564200-13608400	Weak transcription	HSMM	muscle
15	chr20:13564400-13584400	Weak transcription	Rectal Mucosa Donor 29	rectum
16	chr20:13567200-13608600	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr20:13567200-13618600	Weak transcription	Adipose Nuclei	Adipose
18	chr20:13567400-13583800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
19	chr20:13567400-13583800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr20:13567400-13584000	Weak transcription	Fetal Lung	lung
21	chr20:13567400-13589200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
22	chr20:13567400-13594400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr20:13567400-13597400	Weak transcription	Duodenum Mucosa	Duodenum
24	chr20:13567400-13602800	Weak transcription	A549	lung
25	chr20:13567400-13606400	Weak transcription	Primary B cells from peripheral blood	blood
26	chr20:13567400-13608400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr20:13567400-13608400	Weak transcription	HMEC	breast
28	chr20:13567600-13608600	Weak transcription	Fetal Muscle Trunk	muscle
29	chr20:13568000-13608400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
30	chr20:13568200-13584400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr20:13568200-13589000	Weak transcription	Primary B cells from cord blood	blood
32	chr20:13568400-13607200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr20:13568600-13589000	Weak transcription	Primary T helper cells fromperipheralblood	blood
34	chr20:13568800-13589200	Weak transcription	HepG2	liver
35	chr20:13568800-13602800	Weak transcription	Fetal Intestine Large	intestine
36	chr20:13569800-13583800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr20:13572000-13607800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
38	chr20:13573600-13609400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
39	chr20:13574200-13606600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
40	chr20:13574400-13585800	Weak transcription	Esophagus	oesophagus
41	chr20:13574400-13606400	Weak transcription	Thymus	Thymus
42	chr20:13574600-13606600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr20:13577400-13590600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr20:13578000-13587600	Weak transcription	Colon Smooth Muscle	Colon
45	chr20:13578000-13588800	Weak transcription	Primary hematopoietic stem cells	blood
46	chr20:13579800-13585000	Genic enhancers	Dnd41	blood
47	chr20:13581000-13595800	Weak transcription	NHEK	skin
48	chr20:13581200-13585200	Weak transcription	Brain Hippocampus Middle	brain
49	chr20:13581200-13606200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
50	chr20:13582000-13603000	Weak transcription	Liver	Liver

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links