Variant report

Variant	rs1973948
Chromosome Location	chr20:13565291-13565292
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 61 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs11698396	1.00[CHB][hapmap];0.91[JPT][hapmap];0.84[ASN][1000 genomes]
rs12329562	0.81[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap]
rs13041649	0.84[ASN][1000 genomes]
rs28444692	0.84[ASN][1000 genomes]
rs2876356	0.93[CHB][hapmap];0.93[JPT][hapmap]
rs3789343	0.93[CHB][hapmap];1.00[JPT][hapmap]
rs3789345	0.93[CHB][hapmap];0.93[JPT][hapmap]
rs3789350	0.93[CHB][hapmap];0.93[JPT][hapmap]
rs4411781	0.93[CHB][hapmap];0.93[JPT][hapmap]
rs6033731	0.93[CHB][hapmap];0.93[JPT][hapmap]
rs6033735	0.93[CHB][hapmap];0.93[JPT][hapmap]
rs6033736	0.93[CHB][hapmap];1.00[JPT][hapmap]
rs6033745	0.93[CHB][hapmap];0.93[JPT][hapmap]
rs6033755	0.93[CHB][hapmap];1.00[JPT][hapmap]
rs6042167	0.93[CHB][hapmap];1.00[JPT][hapmap]
rs6042181	0.93[CHB][hapmap];0.93[JPT][hapmap]
rs6042183	0.93[CHB][hapmap];0.93[JPT][hapmap]
rs6042222	0.93[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs6105115	0.93[CHB][hapmap];0.93[JPT][hapmap]
rs6105116	0.92[CHB][hapmap];0.93[JPT][hapmap]
rs6109913	0.86[CHB][hapmap];0.93[JPT][hapmap]
rs6131480	0.92[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap]
rs6131482	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs6131494	0.86[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs6134882	0.85[CHB][hapmap];0.93[JPT][hapmap]
rs6134883	0.93[CHB][hapmap];0.93[JPT][hapmap]
rs6134885	0.93[CHB][hapmap];1.00[JPT][hapmap]
rs6134890	0.93[CHB][hapmap];0.93[JPT][hapmap]
rs6134892	0.80[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap]
rs6134896	0.93[CHB][hapmap];1.00[JPT][hapmap]
rs6134904	0.93[CHB][hapmap];1.00[JPT][hapmap]
rs6134907	0.80[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs6134908	0.83[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs6134909	0.84[ASN][1000 genomes]
rs6134911	0.83[AFR][1000 genomes];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6134913	0.93[CHB][hapmap];0.82[JPT][hapmap];0.84[ASN][1000 genomes]
rs6134914	0.93[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs6134915	0.84[ASN][1000 genomes]
rs6134918	0.90[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6134928	0.86[CHB][hapmap];0.85[ASN][1000 genomes]
rs6134931	0.85[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs6134941	0.81[CHB][hapmap];0.86[ASN][1000 genomes]
rs7272156	1.00[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs7273818	0.86[CHB][hapmap];0.86[ASN][1000 genomes]
rs73086022	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs73086039	0.80[ASN][1000 genomes]
rs73090125	1.00[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs8115098	0.93[CHB][hapmap];0.93[JPT][hapmap]
rs8126063	0.85[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap]
rs8184309	0.93[CHB][hapmap];1.00[JPT][hapmap];0.84[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
rs1973948	TASP1	cis	lung	GTEx

Chromatin state (count:86 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:13492200-13567000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr20:13515000-13605600	Weak transcription	Primary T helper cells PMA-I stimulated	--
3	chr20:13526800-13613800	Weak transcription	Hela-S3	cervix
4	chr20:13535600-13608000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr20:13538200-13571800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
6	chr20:13541200-13578000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr20:13545000-13567000	Strong transcription	Dnd41	blood
8	chr20:13546200-13594200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr20:13546800-13574000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr20:13547600-13565600	Weak transcription	Osteobl	bone
11	chr20:13548000-13568600	Weak transcription	Brain Angular Gyrus	brain
12	chr20:13548600-13566200	Weak transcription	Duodenum Smooth Muscle	Duodenum
13	chr20:13548600-13568800	Weak transcription	Skeletal Muscle Female	skeletal muscle
14	chr20:13548600-13584600	Weak transcription	Gastric	stomach
15	chr20:13554000-13568400	Weak transcription	Fetal Brain Male	brain
16	chr20:13554600-13577400	Weak transcription	Monocytes-CD14+_RO01746	blood
17	chr20:13554800-13567000	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr20:13556000-13565600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr20:13556200-13618800	Weak transcription	Skeletal Muscle Male	skeletal muscle
20	chr20:13556600-13565400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr20:13556600-13567000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr20:13556600-13567000	Weak transcription	Psoas Muscle	Psoas
23	chr20:13556600-13567800	Weak transcription	Liver	Liver
24	chr20:13556800-13566200	Weak transcription	Brain Hippocampus Middle	brain
25	chr20:13556800-13566400	Weak transcription	H1 Cell Line	embryonic stem cell
26	chr20:13557200-13566800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
27	chr20:13557800-13566400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
28	chr20:13561200-13566200	Weak transcription	Fetal Muscle Trunk	muscle
29	chr20:13561600-13566000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
30	chr20:13561800-13567000	Weak transcription	Primary T helper cells fromperipheralblood	blood
31	chr20:13563400-13565400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr20:13563400-13567200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr20:13563400-13571200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr20:13563800-13566400	Weak transcription	Sigmoid Colon	Sigmoid Colon
35	chr20:13563800-13568400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
36	chr20:13563800-13619000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr20:13564000-13565600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
38	chr20:13564000-13566200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
39	chr20:13564000-13566400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
40	chr20:13564000-13566600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr20:13564000-13566600	Weak transcription	Primary hematopoietic stem cells	blood
42	chr20:13564000-13566600	Weak transcription	Adipose Nuclei	Adipose
43	chr20:13564000-13566800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
44	chr20:13564000-13567000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr20:13564000-13567000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
46	chr20:13564000-13567000	Weak transcription	Stomach Smooth Muscle	stomach
47	chr20:13564000-13567800	Weak transcription	Fetal Muscle Leg	muscle
48	chr20:13564000-13567800	Weak transcription	Left Ventricle	heart
49	chr20:13564000-13569000	Weak transcription	NH-A	brain
50	chr20:13564000-13574000	Weak transcription	Esophagus	oesophagus

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links