Variant report

Variant	rs6042269
Chromosome Location	chr20:13618093-13618094
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr20:13612016..13613555-chr20:13616672..13619418,2	MCF-7	breast:

Extended variants
information (count: 48 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs2070307	0.88[CHB][hapmap];0.94[JPT][hapmap];0.97[ASN][1000 genomes]
rs2070308	0.93[CHB][hapmap];0.94[JPT][hapmap];0.97[ASN][1000 genomes]
rs2180569	0.93[YRI][hapmap];0.82[AFR][1000 genomes]
rs2295505	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2295506	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2423729	0.86[CHB][hapmap];0.94[JPT][hapmap];0.97[ASN][1000 genomes]
rs2423730	0.88[CHB][hapmap];0.94[JPT][hapmap];0.95[ASN][1000 genomes]
rs2423731	0.88[CHB][hapmap];0.94[JPT][hapmap];0.95[ASN][1000 genomes]
rs34146992	0.85[AFR][1000 genomes]
rs34920916	0.86[EUR][1000 genomes]
rs6033772	1.00[CEU][hapmap];0.93[CHB][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6033773	0.97[ASN][1000 genomes]
rs6033777	0.94[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6033778	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6033779	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6042236	0.96[YRI][hapmap];0.87[AFR][1000 genomes]
rs6042240	0.90[YRI][hapmap];0.85[AFR][1000 genomes]
rs6042245	0.93[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6042255	0.97[ASN][1000 genomes]
rs6042256	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6042261	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6042262	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]
rs6042263	0.87[CHB][hapmap];0.94[JPT][hapmap];0.97[ASN][1000 genomes]
rs6042266	0.95[ASN][1000 genomes]
rs6105142	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6109979	0.97[ASN][1000 genomes]
rs6131494	0.95[EUR][1000 genomes]
rs6131495	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6134928	0.93[CEU][hapmap];0.88[EUR][1000 genomes]
rs6134930	0.96[YRI][hapmap];0.87[AFR][1000 genomes]
rs6134931	0.88[EUR][1000 genomes]
rs6134935	0.89[AFR][1000 genomes]
rs6134937	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6134938	0.80[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6134941	0.94[CEU][hapmap];0.95[EUR][1000 genomes]
rs6514424	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7272156	0.95[EUR][1000 genomes]
rs7273818	0.93[CEU][hapmap];0.95[EUR][1000 genomes]
rs73088095	0.82[EUR][1000 genomes]
rs73090125	0.93[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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	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
6	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
7	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
8	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
rs6042269	TASP1	cis	lung	GTEx
rs6042269	ISM1	cis	lung	GTEx

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:13556200-13618800	Weak transcription	Skeletal Muscle Male	skeletal muscle
2	chr20:13563800-13619000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr20:13567200-13618600	Weak transcription	Adipose Nuclei	Adipose
4	chr20:13588000-13618600	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr20:13591200-13619000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
6	chr20:13594400-13618600	Weak transcription	Brain Cingulate Gyrus	brain
7	chr20:13595400-13618200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
8	chr20:13595600-13618200	Weak transcription	Colon Smooth Muscle	Colon
9	chr20:13596200-13618200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
10	chr20:13597400-13618800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr20:13598200-13618800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr20:13599000-13618600	Weak transcription	Fetal Intestine Small	intestine
13	chr20:13601000-13618400	Weak transcription	NHLF	lung
14	chr20:13601600-13618200	Weak transcription	Brain Germinal Matrix	brain
15	chr20:13602000-13618200	Weak transcription	Skeletal Muscle Female	skeletal muscle
16	chr20:13603600-13618600	Weak transcription	Rectal Mucosa Donor 29	rectum
17	chr20:13605800-13618800	Weak transcription	Colonic Mucosa	Colon
18	chr20:13605800-13619000	Weak transcription	Spleen	Spleen
19	chr20:13606400-13618200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr20:13606800-13618200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr20:13607000-13618800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr20:13607400-13618800	Weak transcription	H9 Cell Line	embryonic stem cell
23	chr20:13607600-13618800	Weak transcription	Placenta	Placenta
24	chr20:13607800-13618400	Weak transcription	Pancreatic Islets	Pancreatic Islet
25	chr20:13608200-13618400	Weak transcription	H1 Cell Line	embryonic stem cell
26	chr20:13608800-13618400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
27	chr20:13608800-13618600	Weak transcription	Muscle Satellite Cultured Cells	--
28	chr20:13608800-13618800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr20:13608800-13618800	Weak transcription	HSMM	muscle
30	chr20:13609000-13618200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr20:13609000-13618800	Weak transcription	HSMMtube	muscle
32	chr20:13609200-13618200	Weak transcription	HMEC	breast
33	chr20:13609200-13618600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
34	chr20:13609200-13618600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr20:13609400-13618600	Weak transcription	Primary hematopoietic stem cells	blood
36	chr20:13609600-13618200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr20:13609600-13618200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
38	chr20:13609600-13618200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr20:13609600-13618200	Weak transcription	Fetal Lung	lung
40	chr20:13609600-13618600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
41	chr20:13609600-13618600	Weak transcription	Stomach Smooth Muscle	stomach
42	chr20:13609600-13618800	Weak transcription	Primary T cells fromperipheralblood	blood
43	chr20:13609600-13618800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
44	chr20:13609600-13618800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
45	chr20:13609600-13618800	Weak transcription	Brain Hippocampus Middle	brain
46	chr20:13609600-13618800	Weak transcription	Brain Inferior Temporal Lobe	brain
47	chr20:13609600-13618800	Weak transcription	Monocytes-CD14+_RO01746	blood
48	chr20:13609800-13618200	Weak transcription	Duodenum Mucosa	Duodenum
49	chr20:13609800-13618200	Weak transcription	Duodenum Smooth Muscle	Duodenum
50	chr20:13609800-13618200	Weak transcription	Rectal Mucosa Donor 31	rectum

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