Variant report

Variant	rs2474776
Chromosome Location	chr20:25270734-25270735
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr20:25270242-25271112	PANC-1	pancreas:	n/a	n/a
2	POLR2A	chr20:25270559-25271191	HepG2	liver:	n/a	n/a
3	POLR2A	chr20:25270585-25278923	Hela-S3	cervix:	n/a	n/a
4	POLR2A	chr20:25270332-25278907	A549	lung:	n/a	n/a
5	POLR2A	chr20:25270412-25273689	A549	lung:	n/a	n/a
6	CREB1	chr20:25270668-25271130	A549	lung:	n/a	n/a

Variant related genes	Relation type
PYGB	TF binding region

Extended variants
information (count: 90 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs2039400	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2258671	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2258672	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2474768	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2474770	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2474772	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2474775	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2482907	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2482909	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2482916	1.00[AMR][1000 genomes]
rs2482917	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2482920	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2482922	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2482925	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2482929	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2482939	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2482942	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2482945	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2500394	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2500396	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2500402	1.00[AMR][1000 genomes]
rs2500407	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2500409	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2500411	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2500412	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2500414	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2500416	1.00[ASN][1000 genomes]
rs2500419	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2500420	1.00[AMR][1000 genomes]
rs2500428	1.00[ASN][1000 genomes]
rs2500429	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2500431	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2500434	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2500435	0.81[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs2500437	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2500438	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2500440	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2500444	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2500445	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2500447	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2983490	1.00[AMR][1000 genomes]
rs2990514	1.00[ASN][1000 genomes]
rs2990515	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3002699	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3002700	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3002703	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs364722	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs368636	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs380021	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs384336	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs426143	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs428801	1.00[ASN][1000 genomes]
rs429120	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs432403	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs448866	1.00[AMR][1000 genomes]
rs56165312	1.00[ASN][1000 genomes]
rs6037089	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6037112	1.00[ASN][1000 genomes]
rs6037113	1.00[ASN][1000 genomes]
rs6037119	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs60483717	1.00[ASN][1000 genomes]
rs6050591	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6050613	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6050618	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6050627	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6050628	1.00[ASN][1000 genomes]
rs73904036	1.00[AMR][1000 genomes]
rs73904038	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73904039	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73904476	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73907308	1.00[ASN][1000 genomes]
rs73907312	1.00[ASN][1000 genomes]
rs73907315	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1062140	chr20:24807962-25304054	Strong transcription Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
2	nsv544219	chr20:24807962-25304054	Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Active TSS Enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	nsv1055341	chr20:24848416-25302271	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
4	nsv1063494	chr20:25067286-25468557	Enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
5	nsv1063016	chr20:25067286-25475629	Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
6	nsv1065101	chr20:25068046-25466542	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
7	nsv544220	chr20:25068046-25466542	Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
8	nsv531480	chr20:25070067-25472684	Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
9	nsv585746	chr20:25071454-25470056	Weak transcription Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
10	nsv1062742	chr20:25071454-25475629	Enhancers Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
11	nsv949389	chr20:25071454-25506582	Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
12	nsv531481	chr20:25080583-25448944	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
13	nsv949479	chr20:25096494-25467359	Weak transcription Enhancers Bivalent Enhancer Strong transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
14	nsv1061109	chr20:25101715-25472685	Enhancers Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
15	nsv544221	chr20:25101715-25472685	Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
16	nsv833948	chr20:25231726-25410540	Strong transcription Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
17	esv1798601	chr20:25250122-25305949	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:25230400-25291600	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr20:25235600-25291200	Weak transcription	Fetal Kidney	kidney
3	chr20:25241800-25273200	Weak transcription	Stomach Mucosa	stomach
4	chr20:25247600-25277400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr20:25249000-25280200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr20:25249200-25274800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr20:25249200-25275000	Strong transcription	A549	lung
8	chr20:25249200-25285800	Strong transcription	Dnd41	blood
9	chr20:25249400-25274600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr20:25249400-25274800	Strong transcription	Osteobl	bone
11	chr20:25249400-25276200	Strong transcription	Fetal Intestine Large	intestine
12	chr20:25249600-25273400	Strong transcription	NHEK	skin
13	chr20:25249600-25274400	Strong transcription	Lung	lung
14	chr20:25249600-25274600	Strong transcription	Primary T cells from cord blood	blood
15	chr20:25249600-25274600	Strong transcription	Duodenum Mucosa	Duodenum
16	chr20:25249600-25274800	Strong transcription	Primary T helper cells fromperipheralblood	blood
17	chr20:25249600-25275000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr20:25249600-25275000	Strong transcription	Cortex derived primary cultured neurospheres	brain
19	chr20:25249600-25275000	Strong transcription	NHLF	lung
20	chr20:25249600-25275200	Strong transcription	Rectal Mucosa Donor 29	rectum
21	chr20:25249600-25279000	Strong transcription	Sigmoid Colon	Sigmoid Colon
22	chr20:25249600-25279400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr20:25249600-25284800	Strong transcription	Primary monocytes fromperipheralblood	blood
24	chr20:25249600-25285200	Strong transcription	Monocytes-CD14+_RO01746	blood
25	chr20:25249800-25273200	Strong transcription	Primary neutrophils fromperipheralblood	blood
26	chr20:25249800-25273400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr20:25249800-25273400	Strong transcription	Primary T helper cells PMA-I stimulated	--
28	chr20:25249800-25274000	Strong transcription	HUES6 Cell Line	embryonic stem cell
29	chr20:25249800-25274600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
30	chr20:25249800-25274600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr20:25249800-25275000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr20:25249800-25275200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
33	chr20:25249800-25275200	Strong transcription	Fetal Stomach	stomach
34	chr20:25249800-25276400	Strong transcription	Fetal Intestine Small	intestine
35	chr20:25249800-25284400	Strong transcription	Brain Germinal Matrix	brain
36	chr20:25250000-25273000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr20:25250000-25274800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
38	chr20:25250000-25274800	Strong transcription	Placenta Amnion	Placenta Amnion
39	chr20:25250000-25275800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr20:25250600-25276200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr20:25250800-25285000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr20:25251400-25275400	Strong transcription	Thymus	Thymus
43	chr20:25252200-25276400	Weak transcription	Hela-S3	cervix
44	chr20:25253800-25273800	Strong transcription	Duodenum Smooth Muscle	Duodenum
45	chr20:25254000-25276200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr20:25254200-25274600	Weak transcription	Psoas Muscle	Psoas
47	chr20:25254200-25275000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr20:25254400-25271200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
49	chr20:25254400-25287800	Weak transcription	K562	blood
50	chr20:25254800-25272600	Strong transcription	Brain Substantia Nigra	brain

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