Variant report

Variant	rs6042225
Chromosome Location	chr20:13566049-13566050
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 83 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs1040756	0.84[CHB][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs13040087	0.92[ASN][1000 genomes]
rs13042843	0.82[JPT][hapmap]
rs2057259	0.95[CHB][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs2070305	0.82[JPT][hapmap]
rs2103972	0.82[AFR][1000 genomes]
rs2180569	1.00[CHB][hapmap];0.95[JPT][hapmap];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2182708	0.81[AFR][1000 genomes]
rs2208208	0.81[AFR][1000 genomes]
rs2273480	0.81[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs2295503	0.81[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs2295504	1.00[CHB][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs2327793	0.83[ASN][1000 genomes]
rs2423732	0.88[ASN][1000 genomes]
rs2423733	0.89[ASN][1000 genomes]
rs2423734	0.89[ASN][1000 genomes]
rs2423736	0.83[ASN][1000 genomes]
rs2423737	0.86[ASN][1000 genomes]
rs2423738	0.83[ASN][1000 genomes]
rs2423739	0.83[ASN][1000 genomes]
rs34146992	0.92[ASN][1000 genomes]
rs34822601	0.80[ASN][1000 genomes]
rs3747931	0.87[YRI][hapmap]
rs3789342	0.84[JPT][hapmap];0.94[YRI][hapmap]
rs3789349	0.94[YRI][hapmap]
rs4441543	0.82[ASN][1000 genomes]
rs4813131	0.81[JPT][hapmap];1.00[YRI][hapmap]
rs4814242	1.00[YRI][hapmap];0.86[AFR][1000 genomes]
rs57218913	0.81[AFR][1000 genomes]
rs6033766	0.92[ASN][1000 genomes]
rs6033767	0.94[ASN][1000 genomes]
rs6033768	1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs6033783	0.93[ASN][1000 genomes]
rs6033795	0.87[ASN][1000 genomes]
rs6042235	0.83[ASN][1000 genomes]
rs6042236	1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs6042239	1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs6042240	1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs6042264	0.91[ASN][1000 genomes]
rs6042273	0.90[ASN][1000 genomes]
rs6042285	0.84[ASN][1000 genomes]
rs6042301	0.85[CHB][hapmap];0.86[JPT][hapmap]
rs6074618	0.81[AFR][1000 genomes]
rs6074627	0.82[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes]
rs6079063	0.83[YRI][hapmap]
rs6079066	0.82[JPT][hapmap];1.00[YRI][hapmap]
rs6079072	1.00[YRI][hapmap]
rs6079075	1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs6079077	0.81[JPT][hapmap];1.00[YRI][hapmap]
rs6079085	0.81[AFR][1000 genomes]
rs6079106	0.81[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes]
rs6105096	1.00[YRI][hapmap]
rs6105103	1.00[YRI][hapmap]
rs6105137	0.89[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs6109891	0.81[AFR][1000 genomes]
rs6109905	0.82[JPT][hapmap];1.00[YRI][hapmap]
rs6109958	0.82[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes]
rs6109983	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs6109990	0.85[ASN][1000 genomes]
rs6109993	0.86[ASN][1000 genomes]
rs6109995	0.84[ASN][1000 genomes]
rs6131483	0.82[JPT][hapmap];1.00[YRI][hapmap]
rs6131488	0.82[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes]
rs6131499	0.81[ASN][1000 genomes]
rs6134879	0.81[AFR][1000 genomes]
rs6134902	0.84[AFR][1000 genomes]
rs6134919	0.89[CHB][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs6134930	1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs6134935	0.92[ASN][1000 genomes]
rs6134948	0.88[ASN][1000 genomes]
rs6514418	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73086013	0.84[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 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

No data

Chromatin state (count:82 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:13492200-13567000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr20:13515000-13605600	Weak transcription	Primary T helper cells PMA-I stimulated	--
3	chr20:13526800-13613800	Weak transcription	Hela-S3	cervix
4	chr20:13535600-13608000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr20:13538200-13571800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
6	chr20:13541200-13578000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr20:13545000-13567000	Strong transcription	Dnd41	blood
8	chr20:13546200-13594200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr20:13546800-13574000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr20:13548000-13568600	Weak transcription	Brain Angular Gyrus	brain
11	chr20:13548600-13566200	Weak transcription	Duodenum Smooth Muscle	Duodenum
12	chr20:13548600-13568800	Weak transcription	Skeletal Muscle Female	skeletal muscle
13	chr20:13548600-13584600	Weak transcription	Gastric	stomach
14	chr20:13554000-13568400	Weak transcription	Fetal Brain Male	brain
15	chr20:13554600-13577400	Weak transcription	Monocytes-CD14+_RO01746	blood
16	chr20:13554800-13567000	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr20:13556200-13618800	Weak transcription	Skeletal Muscle Male	skeletal muscle
18	chr20:13556600-13567000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr20:13556600-13567000	Weak transcription	Psoas Muscle	Psoas
20	chr20:13556600-13567800	Weak transcription	Liver	Liver
21	chr20:13556800-13566200	Weak transcription	Brain Hippocampus Middle	brain
22	chr20:13556800-13566400	Weak transcription	H1 Cell Line	embryonic stem cell
23	chr20:13557200-13566800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
24	chr20:13557800-13566400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
25	chr20:13561200-13566200	Weak transcription	Fetal Muscle Trunk	muscle
26	chr20:13561800-13567000	Weak transcription	Primary T helper cells fromperipheralblood	blood
27	chr20:13563400-13567200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr20:13563400-13571200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr20:13563800-13566400	Weak transcription	Sigmoid Colon	Sigmoid Colon
30	chr20:13563800-13568400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
31	chr20:13563800-13619000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr20:13564000-13566200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
33	chr20:13564000-13566400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
34	chr20:13564000-13566600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr20:13564000-13566600	Weak transcription	Primary hematopoietic stem cells	blood
36	chr20:13564000-13566600	Weak transcription	Adipose Nuclei	Adipose
37	chr20:13564000-13566800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
38	chr20:13564000-13567000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr20:13564000-13567000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
40	chr20:13564000-13567000	Weak transcription	Stomach Smooth Muscle	stomach
41	chr20:13564000-13567800	Weak transcription	Fetal Muscle Leg	muscle
42	chr20:13564000-13567800	Weak transcription	Left Ventricle	heart
43	chr20:13564000-13569000	Weak transcription	NH-A	brain
44	chr20:13564000-13574000	Weak transcription	Esophagus	oesophagus
45	chr20:13564000-13575000	Weak transcription	Spleen	Spleen
46	chr20:13564000-13583400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr20:13564000-13602600	Weak transcription	Ovary	ovary
48	chr20:13564000-13612400	Weak transcription	Pancreas	Pancrea
49	chr20:13564200-13567000	Weak transcription	Duodenum Mucosa	Duodenum
50	chr20:13564200-13567000	Weak transcription	NHEK	skin

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