Variant report

Variant	rs6042222
Chromosome Location	chr20:13557267-13557268
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr20:13556269..13557817-chr20:13617779..13619748,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000089123	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs11698396	1.00[CHB][hapmap];0.91[JPT][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12329562	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13041649	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1973948	0.93[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs28444692	0.80[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2876356	1.00[CHB][hapmap];0.93[JPT][hapmap];0.80[YRI][hapmap]
rs3789343	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.81[TSI][hapmap];0.88[YRI][hapmap]
rs3789345	1.00[CHB][hapmap];0.93[JPT][hapmap];0.80[YRI][hapmap]
rs3789350	1.00[CHB][hapmap];0.96[CHD][hapmap];0.84[GIH][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap]
rs4411781	1.00[CHB][hapmap];0.93[JPT][hapmap]
rs6033731	1.00[ASW][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.84[GIH][hapmap];0.93[JPT][hapmap];0.92[MKK][hapmap];0.80[YRI][hapmap]
rs6033735	1.00[ASW][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.84[GIH][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.80[YRI][hapmap]
rs6033736	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs6033745	1.00[CHB][hapmap];0.96[CHD][hapmap];0.84[GIH][hapmap];0.93[JPT][hapmap];0.93[MEX][hapmap]
rs6033755	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[ASN][1000 genomes]
rs6042167	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap]
rs6042181	1.00[CHB][hapmap];0.93[JPT][hapmap];0.80[YRI][hapmap]
rs6042183	1.00[CHB][hapmap];0.96[CHD][hapmap];0.84[GIH][hapmap];0.93[JPT][hapmap];0.93[MEX][hapmap]
rs6105115	1.00[ASW][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.84[GIH][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.80[YRI][hapmap]
rs6105116	1.00[CHB][hapmap];0.93[JPT][hapmap];0.89[YRI][hapmap]
rs6109913	1.00[ASW][hapmap];0.93[CHB][hapmap];0.92[CHD][hapmap];0.84[GIH][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap]
rs6131480	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6131482	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap]
rs6134882	0.92[CHB][hapmap];0.93[JPT][hapmap]
rs6134883	1.00[CHB][hapmap];0.93[JPT][hapmap]
rs6134885	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap]
rs6134890	1.00[ASW][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.84[GIH][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.80[YRI][hapmap]
rs6134892	1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap]
rs6134896	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap]
rs6134904	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.84[TSI][hapmap];1.00[YRI][hapmap];0.83[ASN][1000 genomes]
rs6134907	1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs6134908	0.84[ASN][1000 genomes]
rs6134909	0.91[ASN][1000 genomes]
rs6134911	0.91[ASN][1000 genomes]
rs6134913	0.86[ASW][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];0.83[GIH][hapmap];0.82[JPT][hapmap];0.84[TSI][hapmap];0.91[ASN][1000 genomes]
rs6134914	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6134915	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6134918	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs73086022	0.91[ASN][1000 genomes]
rs73086039	0.87[ASN][1000 genomes]
rs8115098	1.00[CHB][hapmap];0.93[JPT][hapmap]
rs8126063	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs8184309	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[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
rs6042222	TASP1	cis	lung	GTEx

Chromatin state (count:95 , 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	chr20:13497800-13563400	Weak transcription	Pancreas	Pancrea
3	chr20:13506400-13558800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
4	chr20:13508000-13563600	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr20:13508400-13559600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr20:13508400-13563400	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr20:13515000-13605600	Weak transcription	Primary T helper cells PMA-I stimulated	--
8	chr20:13526800-13561800	Weak transcription	Stomach Mucosa	stomach
9	chr20:13526800-13613800	Weak transcription	Hela-S3	cervix
10	chr20:13527400-13560000	Weak transcription	HSMMtube	muscle
11	chr20:13527400-13562200	Weak transcription	Aorta	Aorta
12	chr20:13527400-13563400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr20:13527600-13559600	Weak transcription	HMEC	breast
14	chr20:13527800-13563400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr20:13534600-13563600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
16	chr20:13534600-13563600	Weak transcription	Lung	lung
17	chr20:13535000-13559600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
18	chr20:13535000-13563400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
19	chr20:13535200-13560200	Weak transcription	Rectal Mucosa Donor 29	rectum
20	chr20:13535600-13608000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr20:13535800-13561400	Weak transcription	NHEK	skin
22	chr20:13536800-13563400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
23	chr20:13537400-13563600	Weak transcription	Placenta	Placenta
24	chr20:13538200-13571800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
25	chr20:13539000-13560600	Weak transcription	Thymus	Thymus
26	chr20:13541200-13578000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr20:13541400-13557600	Weak transcription	Primary T helper cells fromperipheralblood	blood
28	chr20:13541800-13558200	Weak transcription	Primary B cells from peripheral blood	blood
29	chr20:13544200-13563600	Weak transcription	Cortex derived primary cultured neurospheres	brain
30	chr20:13545000-13567000	Strong transcription	Dnd41	blood
31	chr20:13546200-13594200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr20:13546400-13563400	Weak transcription	Fetal Brain Female	brain
33	chr20:13546800-13574000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
34	chr20:13547600-13565600	Weak transcription	Osteobl	bone
35	chr20:13547800-13563600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr20:13547800-13563600	Weak transcription	Fetal Kidney	kidney
37	chr20:13548000-13560600	Weak transcription	Primary T cells fromperipheralblood	blood
38	chr20:13548000-13563400	Weak transcription	Pancreatic Islets	Pancreatic Islet
39	chr20:13548000-13568600	Weak transcription	Brain Angular Gyrus	brain
40	chr20:13548600-13563600	Weak transcription	Duodenum Mucosa	Duodenum
41	chr20:13548600-13566200	Weak transcription	Duodenum Smooth Muscle	Duodenum
42	chr20:13548600-13568800	Weak transcription	Skeletal Muscle Female	skeletal muscle
43	chr20:13548600-13584600	Weak transcription	Gastric	stomach
44	chr20:13548800-13557600	Weak transcription	Primary B cells from cord blood	blood
45	chr20:13549000-13563400	Weak transcription	NH-A	brain
46	chr20:13551200-13563400	Weak transcription	Stomach Smooth Muscle	stomach
47	chr20:13551600-13563600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr20:13551800-13563400	Weak transcription	Esophagus	oesophagus
49	chr20:13553000-13563400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr20:13553600-13557400	Weak transcription	Primary T cells from cord blood	blood

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