Variant report

Variant	rs6109967
Chromosome Location	chr20:13571853-13571854
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 39 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10439586	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2094652	1.00[MEX][hapmap]
rs2180570	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4239710	1.00[MEX][hapmap]
rs6033774	1.00[YRI][hapmap];0.98[AFR][1000 genomes]
rs6033782	1.00[YRI][hapmap];0.98[AFR][1000 genomes]
rs6033784	0.93[AFR][1000 genomes]
rs6042233	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6042234	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6042237	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6042241	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6042242	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6042243	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6042246	0.98[AFR][1000 genomes]
rs6042247	1.00[ASW][hapmap];1.00[LWK][hapmap];0.91[YRI][hapmap];0.98[AFR][1000 genomes]
rs6042248	0.98[AFR][1000 genomes]
rs6042249	0.98[AFR][1000 genomes]
rs6042252	0.98[AFR][1000 genomes]
rs6042265	1.00[YRI][hapmap];0.98[AFR][1000 genomes]
rs6042267	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes]
rs6042334	1.00[MEX][hapmap]
rs6074639	1.00[MEX][hapmap]
rs6109968	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6109972	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes]
rs6109973	1.00[YRI][hapmap];0.98[AFR][1000 genomes]
rs6109985	1.00[YRI][hapmap];0.98[AFR][1000 genomes]
rs73268992	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 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
12	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

No data

Chromatin state (count:58 , 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	chr20:13541200-13578000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr20:13546200-13594200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr20:13546800-13574000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr20:13548600-13584600	Weak transcription	Gastric	stomach
8	chr20:13554600-13577400	Weak transcription	Monocytes-CD14+_RO01746	blood
9	chr20:13556200-13618800	Weak transcription	Skeletal Muscle Male	skeletal muscle
10	chr20:13563800-13619000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr20:13564000-13574000	Weak transcription	Esophagus	oesophagus
12	chr20:13564000-13575000	Weak transcription	Spleen	Spleen
13	chr20:13564000-13583400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr20:13564000-13602600	Weak transcription	Ovary	ovary
15	chr20:13564000-13612400	Weak transcription	Pancreas	Pancrea
16	chr20:13564200-13574000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr20:13564200-13583200	Weak transcription	Aorta	Aorta
18	chr20:13564200-13591000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr20:13564200-13592400	Weak transcription	Cortex derived primary cultured neurospheres	brain
20	chr20:13564200-13602400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
21	chr20:13564200-13602800	Weak transcription	Rectal Mucosa Donor 31	rectum
22	chr20:13564200-13608400	Weak transcription	HSMM	muscle
23	chr20:13564400-13584400	Weak transcription	Rectal Mucosa Donor 29	rectum
24	chr20:13564800-13573800	Weak transcription	Fetal Stomach	stomach
25	chr20:13566600-13572600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
26	chr20:13566800-13574200	Weak transcription	H1 Cell Line	embryonic stem cell
27	chr20:13567200-13572600	Weak transcription	Duodenum Smooth Muscle	Duodenum
28	chr20:13567200-13573800	Weak transcription	Thymus	Thymus
29	chr20:13567200-13574000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr20:13567200-13608600	Weak transcription	Sigmoid Colon	Sigmoid Colon
31	chr20:13567200-13618600	Weak transcription	Adipose Nuclei	Adipose
32	chr20:13567400-13583800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
33	chr20:13567400-13583800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr20:13567400-13584000	Weak transcription	Fetal Lung	lung
35	chr20:13567400-13589200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
36	chr20:13567400-13594400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr20:13567400-13597400	Weak transcription	Duodenum Mucosa	Duodenum
38	chr20:13567400-13602800	Weak transcription	A549	lung
39	chr20:13567400-13606400	Weak transcription	Primary B cells from peripheral blood	blood
40	chr20:13567400-13608400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr20:13567400-13608400	Weak transcription	HMEC	breast
42	chr20:13567600-13608600	Weak transcription	Fetal Muscle Trunk	muscle
43	chr20:13568000-13574000	Weak transcription	Left Ventricle	heart
44	chr20:13568000-13575000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr20:13568000-13583000	Weak transcription	Primary T cells from cord blood	blood
46	chr20:13568000-13608400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
47	chr20:13568200-13582800	Weak transcription	Fetal Thymus	thymus
48	chr20:13568200-13584400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr20:13568200-13589000	Weak transcription	Primary B cells from cord blood	blood
50	chr20:13568400-13607200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood

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