Variant report

Variant	rs6042262
Chromosome Location	chr20:13607555-13607556
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr20:13604911..13607863-chr20:13611443..13613306,2	K562	blood:
2	chr20:13606363..13608023-chr20:13611661..13613306,2	K562	blood:
3	chr20:13606234..13607847-chr20:13615873..13617564,2	K562	blood:

Extended variants
information (count: 51 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs2057259	0.91[LWK][hapmap]
rs2070307	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2070308	1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.94[ASN][1000 genomes]
rs2070334	0.80[LWK][hapmap]
rs2180569	0.83[YRI][hapmap]
rs2295505	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2295506	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2423729	0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.94[ASN][1000 genomes]
rs2423730	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2423731	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs34920916	0.83[EUR][1000 genomes]
rs3789348	0.86[YRI][hapmap]
rs6033772	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.96[GIH][hapmap];0.88[MEX][hapmap];0.81[MKK][hapmap];0.93[TSI][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6033773	0.94[ASN][1000 genomes]
rs6033777	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6033778	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6033779	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.94[MEX][hapmap];0.93[MKK][hapmap];0.90[TSI][hapmap];0.86[YRI][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6042106	0.80[LWK][hapmap]
rs6042236	0.87[LWK][hapmap];0.86[MKK][hapmap];0.83[YRI][hapmap]
rs6042240	0.80[YRI][hapmap]
rs6042245	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6042255	0.94[ASN][1000 genomes]
rs6042256	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6042261	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.94[MEX][hapmap];0.93[MKK][hapmap];0.96[TSI][hapmap];0.86[YRI][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6042263	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs6042266	0.92[ASN][1000 genomes]
rs6042269	0.94[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6105142	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6109979	0.94[ASN][1000 genomes]
rs6131494	0.92[EUR][1000 genomes]
rs6131495	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6134919	0.91[LWK][hapmap]
rs6134928	0.88[CEU][hapmap];0.83[TSI][hapmap];0.84[EUR][1000 genomes]
rs6134930	0.89[LWK][hapmap];0.86[MKK][hapmap];0.83[YRI][hapmap]
rs6134931	0.84[EUR][1000 genomes]
rs6134937	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.85[LWK][hapmap];0.87[MEX][hapmap];0.88[MKK][hapmap];0.93[TSI][hapmap];0.86[YRI][hapmap];0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6134938	0.94[CHB][hapmap];0.82[JPT][hapmap];0.87[MEX][hapmap];0.89[YRI][hapmap];0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6134941	0.88[CEU][hapmap];0.92[EUR][1000 genomes]
rs6514424	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.93[MEX][hapmap];0.93[MKK][hapmap];0.96[TSI][hapmap];0.86[YRI][hapmap];0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7272156	0.92[EUR][1000 genomes]
rs7273818	0.88[CEU][hapmap];0.90[TSI][hapmap];0.92[EUR][1000 genomes]
rs73090125	0.90[EUR][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	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	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
6	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
7	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
8	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
9	nsv1059221	chr20:13589432-13977327	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6042262	TASP1	cis	lung	GTEx
rs6042262	TASP1	cis	cerebellum	SCAN

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:13526800-13613800	Weak transcription	Hela-S3	cervix
2	chr20:13535600-13608000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr20:13556200-13618800	Weak transcription	Skeletal Muscle Male	skeletal muscle
4	chr20:13563800-13619000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr20:13564000-13612400	Weak transcription	Pancreas	Pancrea
6	chr20:13564200-13608400	Weak transcription	HSMM	muscle
7	chr20:13567200-13608600	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr20:13567200-13618600	Weak transcription	Adipose Nuclei	Adipose
9	chr20:13567400-13608400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr20:13567400-13608400	Weak transcription	HMEC	breast
11	chr20:13567600-13608600	Weak transcription	Fetal Muscle Trunk	muscle
12	chr20:13568000-13608400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
13	chr20:13572000-13607800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
14	chr20:13573600-13609400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr20:13582600-13608000	Weak transcription	HSMMtube	muscle
16	chr20:13584000-13617800	Weak transcription	Aorta	Aorta
17	chr20:13585000-13610600	Weak transcription	Psoas Muscle	Psoas
18	chr20:13585200-13609000	Weak transcription	Fetal Muscle Leg	muscle
19	chr20:13586600-13608600	Weak transcription	GM12878-XiMat	blood
20	chr20:13587000-13618000	Weak transcription	Fetal Brain Male	brain
21	chr20:13588000-13618600	Weak transcription	Placenta Amnion	Placenta Amnion
22	chr20:13588600-13609200	Weak transcription	Left Ventricle	heart
23	chr20:13589800-13608400	Weak transcription	Osteobl	bone
24	chr20:13590800-13617800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr20:13591200-13619000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
26	chr20:13592200-13617800	Weak transcription	Small Intestine	intestine
27	chr20:13594400-13618600	Weak transcription	Brain Cingulate Gyrus	brain
28	chr20:13595400-13618200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
29	chr20:13595600-13618200	Weak transcription	Colon Smooth Muscle	Colon
30	chr20:13596000-13607800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr20:13596000-13608400	Weak transcription	Muscle Satellite Cultured Cells	--
32	chr20:13596200-13618200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
33	chr20:13596600-13608800	Weak transcription	Brain Inferior Temporal Lobe	brain
34	chr20:13596600-13609400	Weak transcription	Fetal Brain Female	brain
35	chr20:13596600-13618000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
36	chr20:13597400-13618800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
37	chr20:13597800-13608200	Weak transcription	Duodenum Mucosa	Duodenum
38	chr20:13597800-13608400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr20:13598200-13618800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr20:13599000-13618600	Weak transcription	Fetal Intestine Small	intestine
41	chr20:13600800-13608000	Weak transcription	Fetal Stomach	stomach
42	chr20:13601000-13618400	Weak transcription	NHLF	lung
43	chr20:13601400-13608800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
44	chr20:13601400-13611400	Weak transcription	Brain Substantia Nigra	brain
45	chr20:13601600-13618200	Weak transcription	Brain Germinal Matrix	brain
46	chr20:13602000-13618200	Weak transcription	Skeletal Muscle Female	skeletal muscle
47	chr20:13602800-13610600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr20:13603200-13618000	Weak transcription	Fetal Kidney	kidney
49	chr20:13603400-13608600	Weak transcription	Duodenum Smooth Muscle	Duodenum
50	chr20:13603400-13613600	Genic enhancers	Dnd41	blood

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