Variant report

Variant	rs6042246
Chromosome Location	chr20:13594245-13594246
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 41 )
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[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6033782	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	0.98[AFR][1000 genomes]
rs6042243	0.93[AFR][1000 genomes]
rs6042247	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[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6042267	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	0.98[AFR][1000 genomes]
rs6109968	0.98[AFR][1000 genomes]
rs6109972	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6109973	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6109985	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: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

No data

Chromatin state (count:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:13515000-13605600	Weak transcription	Primary T helper cells PMA-I stimulated	--
2	chr20:13526800-13613800	Weak transcription	Hela-S3	cervix
3	chr20:13535600-13608000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr20:13556200-13618800	Weak transcription	Skeletal Muscle Male	skeletal muscle
5	chr20:13563800-13619000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr20:13564000-13602600	Weak transcription	Ovary	ovary
7	chr20:13564000-13612400	Weak transcription	Pancreas	Pancrea
8	chr20:13564200-13602400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr20:13564200-13602800	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr20:13564200-13608400	Weak transcription	HSMM	muscle
11	chr20:13567200-13608600	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr20:13567200-13618600	Weak transcription	Adipose Nuclei	Adipose
13	chr20:13567400-13594400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr20:13567400-13597400	Weak transcription	Duodenum Mucosa	Duodenum
15	chr20:13567400-13602800	Weak transcription	A549	lung
16	chr20:13567400-13606400	Weak transcription	Primary B cells from peripheral blood	blood
17	chr20:13567400-13608400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr20:13567400-13608400	Weak transcription	HMEC	breast
19	chr20:13567600-13608600	Weak transcription	Fetal Muscle Trunk	muscle
20	chr20:13568000-13608400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
21	chr20:13568400-13607200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr20:13568800-13602800	Weak transcription	Fetal Intestine Large	intestine
23	chr20:13572000-13607800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
24	chr20:13573600-13609400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
25	chr20:13574200-13606600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr20:13574400-13606400	Weak transcription	Thymus	Thymus
27	chr20:13574600-13606600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr20:13581000-13595800	Weak transcription	NHEK	skin
29	chr20:13581200-13606200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
30	chr20:13582000-13603000	Weak transcription	Liver	Liver
31	chr20:13582200-13606200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr20:13582600-13608000	Weak transcription	HSMMtube	muscle
33	chr20:13583200-13602800	Weak transcription	Primary T cells fromperipheralblood	blood
34	chr20:13583200-13607200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
35	chr20:13583200-13607200	Weak transcription	Monocytes-CD14+_RO01746	blood
36	chr20:13583400-13607000	Weak transcription	HUES64 Cell Line	embryonic stem cell
37	chr20:13583800-13605400	Weak transcription	HUES48 Cell Line	embryonic stem cell
38	chr20:13584000-13617800	Weak transcription	Aorta	Aorta
39	chr20:13584200-13594600	Weak transcription	Fetal Stomach	stomach
40	chr20:13585000-13610600	Weak transcription	Psoas Muscle	Psoas
41	chr20:13585200-13602800	Weak transcription	Rectal Mucosa Donor 29	rectum
42	chr20:13585200-13609000	Weak transcription	Fetal Muscle Leg	muscle
43	chr20:13585600-13594600	Weak transcription	Fetal Lung	lung
44	chr20:13585600-13606400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
45	chr20:13586200-13602400	Weak transcription	Fetal Kidney	kidney
46	chr20:13586400-13598600	Weak transcription	Fetal Intestine Small	intestine
47	chr20:13586600-13608600	Weak transcription	GM12878-XiMat	blood
48	chr20:13587000-13597000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr20:13587000-13606400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr20:13587000-13618000	Weak transcription	Fetal Brain Male	brain

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