Variant report

Variant	rs6131494
Chromosome Location	chr20:13609940-13609941
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	chr20:13608491..13611413-chr20:13619029..13620797,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000089123	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs1973948	0.86[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs2295505	0.93[EUR][1000 genomes]
rs2295506	0.93[EUR][1000 genomes]
rs34920916	0.89[EUR][1000 genomes]
rs6033772	0.88[EUR][1000 genomes]
rs6033777	0.90[EUR][1000 genomes]
rs6033778	0.94[EUR][1000 genomes]
rs6033779	0.93[EUR][1000 genomes]
rs6042245	0.86[EUR][1000 genomes]
rs6042256	0.94[EUR][1000 genomes]
rs6042261	0.95[EUR][1000 genomes]
rs6042262	0.92[EUR][1000 genomes]
rs6042269	0.95[EUR][1000 genomes]
rs6105142	0.89[EUR][1000 genomes]
rs6131495	0.95[EUR][1000 genomes]
rs6134918	0.82[AFR][1000 genomes]
rs6134928	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6134931	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6134937	0.89[EUR][1000 genomes]
rs6134938	0.93[EUR][1000 genomes]
rs6134941	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6514424	0.93[EUR][1000 genomes]
rs7272156	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7273818	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73088095	0.86[EUR][1000 genomes]
rs73090125	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[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	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
rs6131494	TASP1	cis	lung	GTEx
rs6131494	ISM1	cis	lung	GTEx

Chromatin state (count:105 , 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	chr20:13556200-13618800	Weak transcription	Skeletal Muscle Male	skeletal muscle
3	chr20:13563800-13619000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr20:13564000-13612400	Weak transcription	Pancreas	Pancrea
5	chr20:13567200-13618600	Weak transcription	Adipose Nuclei	Adipose
6	chr20:13584000-13617800	Weak transcription	Aorta	Aorta
7	chr20:13585000-13610600	Weak transcription	Psoas Muscle	Psoas
8	chr20:13587000-13618000	Weak transcription	Fetal Brain Male	brain
9	chr20:13588000-13618600	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr20:13590800-13617800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr20:13591200-13619000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
12	chr20:13592200-13617800	Weak transcription	Small Intestine	intestine
13	chr20:13594400-13618600	Weak transcription	Brain Cingulate Gyrus	brain
14	chr20:13595400-13618200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
15	chr20:13595600-13618200	Weak transcription	Colon Smooth Muscle	Colon
16	chr20:13596200-13618200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
17	chr20:13596600-13618000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
18	chr20:13597400-13618800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr20:13598200-13618800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr20:13599000-13618600	Weak transcription	Fetal Intestine Small	intestine
21	chr20:13601000-13618400	Weak transcription	NHLF	lung
22	chr20:13601400-13611400	Weak transcription	Brain Substantia Nigra	brain
23	chr20:13601600-13618200	Weak transcription	Brain Germinal Matrix	brain
24	chr20:13602000-13618200	Weak transcription	Skeletal Muscle Female	skeletal muscle
25	chr20:13602800-13610600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr20:13603200-13618000	Weak transcription	Fetal Kidney	kidney
27	chr20:13603400-13613600	Genic enhancers	Dnd41	blood
28	chr20:13603400-13618000	Weak transcription	A549	lung
29	chr20:13603600-13618600	Weak transcription	Rectal Mucosa Donor 29	rectum
30	chr20:13605600-13610800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
31	chr20:13605600-13610800	Strong transcription	Primary T helper cells PMA-I stimulated	--
32	chr20:13605800-13618800	Weak transcription	Colonic Mucosa	Colon
33	chr20:13605800-13619000	Weak transcription	Spleen	Spleen
34	chr20:13606000-13610800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
35	chr20:13606200-13610000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
36	chr20:13606200-13611000	Strong transcription	Primary T helper cells fromperipheralblood	blood
37	chr20:13606400-13610600	Strong transcription	Primary B cells from peripheral blood	blood
38	chr20:13606400-13612000	Weak transcription	Ovary	ovary
39	chr20:13606400-13618200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr20:13606600-13612400	Weak transcription	Lung	lung
41	chr20:13606800-13618200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr20:13607000-13618800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
43	chr20:13607400-13610800	Strong transcription	Primary T cells from cord blood	blood
44	chr20:13607400-13618800	Weak transcription	H9 Cell Line	embryonic stem cell
45	chr20:13607600-13618800	Weak transcription	Placenta	Placenta
46	chr20:13607800-13610800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
47	chr20:13607800-13618400	Weak transcription	Pancreatic Islets	Pancreatic Islet
48	chr20:13608000-13610000	Strong transcription	Fetal Stomach	stomach
49	chr20:13608200-13618400	Weak transcription	H1 Cell Line	embryonic stem cell
50	chr20:13608400-13610000	Strong transcription	Liver	Liver

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