Variant report

Variant	rs4814242
Chromosome Location	chr20:13542423-13542424
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 65 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs13039162	0.86[ASN][1000 genomes]
rs13042843	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2057258	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.81[TSI][hapmap];0.87[ASN][1000 genomes]
rs2070305	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2070334	0.94[CHB][hapmap];0.90[CHD][hapmap];0.90[GIH][hapmap];0.81[TSI][hapmap];0.81[ASN][1000 genomes]
rs2073324	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2103972	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2182708	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2208207	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2208208	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2273480	1.00[ASW][hapmap];0.96[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.92[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3747931	0.96[CEU][hapmap];0.94[CHB][hapmap];0.80[JPT][hapmap];0.86[YRI][hapmap];0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3789342	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3789347	0.94[CHB][hapmap];0.83[ASN][1000 genomes]
rs3789348	1.00[CHB][hapmap];0.83[ASN][1000 genomes]
rs3789349	0.93[YRI][hapmap];0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4813131	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4814236	0.88[ASN][1000 genomes]
rs4814238	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs57218913	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6042106	0.94[CHB][hapmap];0.92[CHD][hapmap];0.92[GIH][hapmap];0.81[TSI][hapmap];0.81[ASN][1000 genomes]
rs6042128	0.94[CHB][hapmap];0.91[JPT][hapmap];0.87[ASN][1000 genomes]
rs6042153	0.86[ASN][1000 genomes]
rs6042225	1.00[YRI][hapmap];0.86[AFR][1000 genomes]
rs6074611	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6074612	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6074613	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6074618	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6074627	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6079058	0.83[CHD][hapmap]
rs6079063	0.83[YRI][hapmap]
rs6079066	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6079072	1.00[ASW][hapmap];0.96[CEU][hapmap];0.94[CHB][hapmap];0.92[CHD][hapmap];0.90[GIH][hapmap];0.80[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6079074	0.94[CHB][hapmap];0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs6079075	0.96[CEU][hapmap];0.94[CHB][hapmap];0.80[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6079077	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];0.95[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6079085	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6079095	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.90[MEX][hapmap];0.91[TSI][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6079106	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.80[GIH][hapmap];0.95[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6105096	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6105098	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6105103	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.90[GIH][hapmap];0.80[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6105113	0.86[ASN][1000 genomes]
rs6109887	0.84[ASN][1000 genomes]
rs6109891	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6109903	0.82[ASN][1000 genomes]
rs6109905	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6109958	1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs6131476	0.83[CHD][hapmap]
rs6131483	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6131485	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6131488	1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs6134879	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6134902	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6134912	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73086013	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4814242	TASP1	cis	parietal	SCAN
rs4814242	TASP1	cis	cerebellum	SCAN

Chromatin state (count:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:13485000-13543600	Weak transcription	Small Intestine	intestine
2	chr20:13492200-13567000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
3	chr20:13497800-13563400	Weak transcription	Pancreas	Pancrea
4	chr20:13506400-13558800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
5	chr20:13508000-13563600	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr20:13508200-13556400	Weak transcription	Fetal Muscle Trunk	muscle
7	chr20:13508400-13546600	Weak transcription	Fetal Kidney	kidney
8	chr20:13508400-13550400	Weak transcription	GM12878-XiMat	blood
9	chr20:13508400-13556000	Weak transcription	HSMM	muscle
10	chr20:13508400-13559600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr20:13508400-13563400	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr20:13509200-13548200	Weak transcription	Duodenum Mucosa	Duodenum
13	chr20:13509200-13556000	Weak transcription	Fetal Stomach	stomach
14	chr20:13509800-13547400	Weak transcription	Primary T cells fromperipheralblood	blood
15	chr20:13512800-13548400	Weak transcription	Left Ventricle	heart
16	chr20:13512800-13556000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
17	chr20:13513800-13547600	Weak transcription	Primary hematopoietic stem cells	blood
18	chr20:13514800-13546400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr20:13515000-13605600	Weak transcription	Primary T helper cells PMA-I stimulated	--
20	chr20:13526800-13561800	Weak transcription	Stomach Mucosa	stomach
21	chr20:13526800-13613800	Weak transcription	Hela-S3	cervix
22	chr20:13527000-13556000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr20:13527400-13552200	Weak transcription	HUES64 Cell Line	embryonic stem cell
24	chr20:13527400-13560000	Weak transcription	HSMMtube	muscle
25	chr20:13527400-13562200	Weak transcription	Aorta	Aorta
26	chr20:13527400-13563400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr20:13527600-13559600	Weak transcription	HMEC	breast
28	chr20:13527800-13563400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr20:13529200-13552200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
30	chr20:13529400-13555800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr20:13530600-13547600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr20:13532400-13547800	Weak transcription	Fetal Lung	lung
33	chr20:13533400-13547000	Weak transcription	A549	lung
34	chr20:13534600-13563600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
35	chr20:13534600-13563600	Weak transcription	Lung	lung
36	chr20:13534800-13552200	Weak transcription	HUES6 Cell Line	embryonic stem cell
37	chr20:13535000-13559600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
38	chr20:13535000-13563400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
39	chr20:13535200-13560200	Weak transcription	Rectal Mucosa Donor 29	rectum
40	chr20:13535400-13547400	Weak transcription	Duodenum Smooth Muscle	Duodenum
41	chr20:13535400-13556400	Weak transcription	Liver	Liver
42	chr20:13535600-13608000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr20:13535800-13547600	Weak transcription	Brain Angular Gyrus	brain
44	chr20:13535800-13552400	Weak transcription	NHDF-Ad	bronchial
45	chr20:13535800-13561400	Weak transcription	NHEK	skin
46	chr20:13536600-13551400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr20:13536600-13556000	Weak transcription	Fetal Muscle Leg	muscle
48	chr20:13536800-13563400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
49	chr20:13537400-13563600	Weak transcription	Placenta	Placenta
50	chr20:13537600-13556000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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