Variant report

Variant	rs6042267
Chromosome Location	chr20:13615053-13615054
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr20:13591529..13593880-chr20:13614121..13615856,2	K562	blood:
2	chr20:13612356..13615929-chr20:13617124..13620591,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000089123	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10439586	0.87[AFR][1000 genomes]
rs13433337	1.00[AMR][1000 genomes]
rs2180570	0.94[AFR][1000 genomes]
rs6033774	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6033782	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6033784	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6033791	1.00[AMR][1000 genomes]
rs6033797	1.00[AMR][1000 genomes]
rs6033800	1.00[AMR][1000 genomes]
rs6042233	0.98[AFR][1000 genomes]
rs6042234	0.98[AFR][1000 genomes]
rs6042237	0.98[AFR][1000 genomes]
rs6042241	0.92[AFR][1000 genomes]
rs6042242	1.00[YRI][hapmap];0.98[AFR][1000 genomes]
rs6042243	0.93[AFR][1000 genomes]
rs6042246	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6042247	1.00[ASW][hapmap];1.00[LWK][hapmap];0.91[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6042248	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6042249	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6042252	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6042265	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6042286	1.00[AMR][1000 genomes]
rs6042298	1.00[AMR][1000 genomes]
rs6042303	1.00[AMR][1000 genomes]
rs6105145	1.00[AMR][1000 genomes]
rs6109967	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes]
rs6109968	0.98[AFR][1000 genomes]
rs6109972	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6109973	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6109985	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73268992	0.83[AFR][1000 genomes]
rs73270770	1.00[AMR][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

No data

Chromatin state (count:97 , 50 per page) page: 1 2

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	chr20:13584000-13617800	Weak transcription	Aorta	Aorta
5	chr20:13587000-13618000	Weak transcription	Fetal Brain Male	brain
6	chr20:13588000-13618600	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr20:13590800-13617800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr20:13591200-13619000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
9	chr20:13592200-13617800	Weak transcription	Small Intestine	intestine
10	chr20:13594400-13618600	Weak transcription	Brain Cingulate Gyrus	brain
11	chr20:13595400-13618200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
12	chr20:13595600-13618200	Weak transcription	Colon Smooth Muscle	Colon
13	chr20:13596200-13618200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
14	chr20:13596600-13618000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
15	chr20:13597400-13618800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr20:13598200-13618800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr20:13599000-13618600	Weak transcription	Fetal Intestine Small	intestine
18	chr20:13601000-13618400	Weak transcription	NHLF	lung
19	chr20:13601600-13618200	Weak transcription	Brain Germinal Matrix	brain
20	chr20:13602000-13618200	Weak transcription	Skeletal Muscle Female	skeletal muscle
21	chr20:13603200-13618000	Weak transcription	Fetal Kidney	kidney
22	chr20:13603400-13618000	Weak transcription	A549	lung
23	chr20:13603600-13618600	Weak transcription	Rectal Mucosa Donor 29	rectum
24	chr20:13605800-13618800	Weak transcription	Colonic Mucosa	Colon
25	chr20:13605800-13619000	Weak transcription	Spleen	Spleen
26	chr20:13606400-13618200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr20:13606800-13618200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr20:13607000-13618800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr20:13607400-13618800	Weak transcription	H9 Cell Line	embryonic stem cell
30	chr20:13607600-13618800	Weak transcription	Placenta	Placenta
31	chr20:13607800-13618400	Weak transcription	Pancreatic Islets	Pancreatic Islet
32	chr20:13608200-13618400	Weak transcription	H1 Cell Line	embryonic stem cell
33	chr20:13608800-13618400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
34	chr20:13608800-13618600	Weak transcription	Muscle Satellite Cultured Cells	--
35	chr20:13608800-13618800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr20:13608800-13618800	Weak transcription	HSMM	muscle
37	chr20:13609000-13618000	Weak transcription	NHEK	skin
38	chr20:13609000-13618200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr20:13609000-13618800	Weak transcription	HSMMtube	muscle
40	chr20:13609200-13617800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr20:13609200-13618000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
42	chr20:13609200-13618200	Weak transcription	HMEC	breast
43	chr20:13609200-13618600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
44	chr20:13609200-13618600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr20:13609400-13617800	Weak transcription	Brain Angular Gyrus	brain
46	chr20:13609400-13618600	Weak transcription	Primary hematopoietic stem cells	blood
47	chr20:13609600-13618200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr20:13609600-13618200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
49	chr20:13609600-13618200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr20:13609600-13618200	Weak transcription	Fetal Lung	lung

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