Variant report

Variant	rs6109919
Chromosome Location	chr20:13496311-13496312
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 53 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs2038436	1.00[AMR][1000 genomes]
rs28445300	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs35357303	1.00[AMR][1000 genomes]
rs3945993	1.00[AMR][1000 genomes]
rs6033700	1.00[AMR][1000 genomes]
rs6033711	1.00[AMR][1000 genomes]
rs6033713	1.00[AMR][1000 genomes]
rs6042062	1.00[AMR][1000 genomes]
rs6042100	1.00[AMR][1000 genomes]
rs6042112	1.00[AMR][1000 genomes]
rs6042114	1.00[AMR][1000 genomes]
rs6042115	1.00[AMR][1000 genomes]
rs6042122	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6042125	1.00[AMR][1000 genomes]
rs6042129	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6042140	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6042144	1.00[AMR][1000 genomes]
rs6042161	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6042166	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6042173	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6042178	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6042191	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6042193	1.00[AMR][1000 genomes]
rs6042200	1.00[AMR][1000 genomes]
rs6042215	1.00[AMR][1000 genomes]
rs6042216	1.00[AMR][1000 genomes]
rs6042217	1.00[AMR][1000 genomes]
rs6105112	1.00[AMR][1000 genomes]
rs6105114	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6105122	1.00[AMR][1000 genomes]
rs6109851	1.00[AMR][1000 genomes]
rs6109852	1.00[AMR][1000 genomes]
rs6109853	1.00[AMR][1000 genomes]
rs6109855	1.00[AMR][1000 genomes]
rs6109856	1.00[AMR][1000 genomes]
rs6109857	1.00[AMR][1000 genomes]
rs6109860	1.00[AMR][1000 genomes]
rs6109874	1.00[AMR][1000 genomes]
rs6109878	1.00[AMR][1000 genomes]
rs6109880	1.00[AMR][1000 genomes]
rs6109881	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6109897	1.00[AMR][1000 genomes]
rs6109943	1.00[AMR][1000 genomes]
rs6109944	1.00[AMR][1000 genomes]
rs6109948	1.00[AMR][1000 genomes]
rs6109956	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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

No data

Chromatin state (count:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:13463800-13505400	Weak transcription	Rectal Mucosa Donor 31	rectum
2	chr20:13470200-13505800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr20:13473400-13505800	Weak transcription	HSMM	muscle
4	chr20:13474400-13496800	Weak transcription	Pancreas	Pancrea
5	chr20:13478200-13503800	Weak transcription	Gastric	stomach
6	chr20:13483200-13509200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
7	chr20:13484000-13499000	Weak transcription	Aorta	Aorta
8	chr20:13484000-13502600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr20:13484000-13502600	Weak transcription	Primary T cells from cord blood	blood
10	chr20:13484000-13502600	Weak transcription	Fetal Stomach	stomach
11	chr20:13484200-13496800	Weak transcription	Left Ventricle	heart
12	chr20:13485000-13502600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr20:13485000-13543600	Weak transcription	Small Intestine	intestine
14	chr20:13485800-13497400	Weak transcription	Primary T helper cells PMA-I stimulated	--
15	chr20:13486200-13502600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr20:13487600-13515000	Weak transcription	Brain Germinal Matrix	brain
17	chr20:13488200-13502600	Weak transcription	Lung	lung
18	chr20:13488200-13502600	Weak transcription	Ovary	ovary
19	chr20:13488600-13496800	Weak transcription	NHEK	skin
20	chr20:13489000-13502600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr20:13489000-13502600	Weak transcription	Primary T cells fromperipheralblood	blood
22	chr20:13489000-13502600	Weak transcription	Fetal Intestine Large	intestine
23	chr20:13489200-13514600	Weak transcription	Brain Inferior Temporal Lobe	brain
24	chr20:13489600-13497600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr20:13489600-13499000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr20:13490400-13502800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr20:13490400-13509600	Weak transcription	Pancreatic Islets	Pancreatic Islet
28	chr20:13490800-13502800	Weak transcription	Rectal Mucosa Donor 29	rectum
29	chr20:13491800-13503400	Weak transcription	Liver	Liver
30	chr20:13492200-13499600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr20:13492200-13503800	Weak transcription	Right Ventricle	heart
32	chr20:13492200-13505600	Weak transcription	Spleen	Spleen
33	chr20:13492200-13567000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
34	chr20:13492600-13502600	Weak transcription	Brain Hippocampus Middle	brain
35	chr20:13492800-13496800	Weak transcription	Sigmoid Colon	Sigmoid Colon
36	chr20:13493600-13496400	ZNF genes & repeats	Dnd41	blood
37	chr20:13493600-13502800	Weak transcription	Duodenum Smooth Muscle	Duodenum
38	chr20:13493600-13505400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
39	chr20:13493600-13507600	Weak transcription	HUES64 Cell Line	embryonic stem cell
40	chr20:13493600-13510800	Weak transcription	Cortex derived primary cultured neurospheres	brain
41	chr20:13493600-13519200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
42	chr20:13493800-13497600	Strong transcription	Primary B cells from cord blood	blood
43	chr20:13493800-13504000	Weak transcription	Fetal Muscle Trunk	muscle
44	chr20:13494000-13502600	Weak transcription	Duodenum Mucosa	Duodenum
45	chr20:13494000-13502600	Weak transcription	A549	lung
46	chr20:13494000-13504000	Weak transcription	Fetal Intestine Small	intestine
47	chr20:13494000-13505400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr20:13494000-13507800	Weak transcription	HUES48 Cell Line	embryonic stem cell
49	chr20:13494000-13512400	Weak transcription	Placenta	Placenta
50	chr20:13494000-13515600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood

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