Variant report

Variant	rs6048205
Chromosome Location	chr20:22559601-22559602
allele	A/G
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	MXI1	chr20:22558275-22559608	HepG2	liver:	n/a	n/a
2	EP300	chr20:22559079-22559726	HepG2	liver:	n/a	chr20:22559388-22559402 chr20:22559384-22559398 chr20:22559383-22559397
3	FOXA2	chr20:22558909-22559857	A549	lung:	n/a	n/a
4	FOSL2	chr20:22559000-22559684	HepG2	liver:	n/a	n/a
5	MBD4	chr20:22558266-22559897	HepG2	liver:	n/a	n/a
6	FOXA1	chr20:22558955-22559712	HepG2	liver:	n/a	n/a
7	CEBPB	chr20:22559239-22559714	HepG2	liver:	n/a	n/a
8	MAX	chr20:22558608-22560119	A549	lung:	n/a	chr20:22559410-22559420
9	TCF12	chr20:22558579-22560178	A549	lung:	n/a	chr20:22559504-22559511 chr20:22559511-22559520
10	FOXA1	chr20:22558981-22559707	HepG2	liver:	n/a	n/a
11	MAX	chr20:22559233-22559990	A549	lung:	n/a	chr20:22559410-22559420
12	MYBL2	chr20:22557536-22559631	HepG2	liver:	n/a	n/a
13	CTBP2	chr20:22557228-22560647	H1-hESC	embryonic stem cell:	n/a	n/a
14	FOXA2	chr20:22558745-22560137	HepG2	liver:	n/a	n/a
15	SP1	chr20:22559100-22559720	HepG2	liver:	n/a	n/a
16	JUND	chr20:22558925-22559609	HepG2	liver:	n/a	n/a
17	POLR2A	chr20:22559164-22559651	H1-neurons	neurons:	n/a	n/a
18	NFIC	chr20:22558778-22559749	HepG2	liver:	n/a	n/a
19	SP1	chr20:22559118-22559764	A549	lung:	n/a	n/a
20	FOXA2	chr20:22559088-22559695	HepG2	liver:	n/a	n/a
21	ARID3A	chr20:22558317-22559671	HepG2	liver:	n/a	n/a
22	JUN	chr20:22559333-22559889	H1-hESC	embryonic stem cell:	n/a	n/a
23	REST	chr20:22559161-22559927	A549	lung:	n/a	n/a
24	MBD4	chr20:22557441-22559690	HepG2	liver:	n/a	n/a
25	MYBL2	chr20:22558961-22559785	HepG2	liver:	n/a	n/a
26	EP300	chr20:22558985-22559719	HepG2	liver:	n/a	chr20:22559388-22559402 chr20:22559384-22559398 chr20:22559383-22559397
27	MAFF	chr20:22559327-22559646	HepG2	liver:	n/a	n/a
28	POLR2A	chr20:22559127-22561986	HepG2	liver:	n/a	n/a
29	TCF7L2	chr20:22559220-22560017	PANC-1	pancreas:	n/a	n/a
30	FOXA1	chr20:22558883-22559837	HepG2	liver:	n/a	n/a
31	FOXA2	chr20:22558843-22559920	A549	lung:	n/a	n/a
32	SP1	chr20:22559148-22559814	A549	lung:	n/a	n/a
33	CEBPB	chr20:22559248-22559843	A549	lung:	n/a	n/a
34	CREB1	chr20:22557536-22559804	HepG2	liver:	n/a	chr20:22559450-22559463
35	HDAC2	chr20:22558094-22559825	HepG2	liver:	n/a	chr20:22559388-22559402 chr20:22559575-22559589 chr20:22559389-22559403 chr20:22559574-22559588 chr20:22559384-22559398 chr20:22559571-22559585 chr20:22559382-22559396 chr20:22559385-22559399 chr20:22559570-22559584 chr20:22559383-22559397 chr20:22559387-22559401
36	SUZ12	chr20:22556202-22561602	NT2-D1	testis:	n/a	n/a
37	POLR2A	chr20:22559128-22559877	H1-neurons	neurons:	n/a	n/a
38	NFIC	chr20:22558294-22559730	HepG2	liver:	n/a	n/a
39	FOXA1	chr20:22558961-22559775	HepG2	liver:	n/a	n/a
40	BCL3	chr20:22559205-22559710	A549	lung:	n/a	n/a
41	POLR2A	chr20:22558301-22561412	PANC-1	pancreas:	n/a	n/a
42	GATA3	chr20:22558944-22559946	A549	lung:	n/a	chr20:22559012-22559020
43	FOSL2	chr20:22559167-22559755	A549	lung:	n/a	n/a
44	EP300	chr20:22559135-22559728	A549	lung:	n/a	chr20:22559388-22559402 chr20:22559384-22559398 chr20:22559383-22559397
45	EP300	chr20:22559142-22559758	A549	lung:	n/a	chr20:22559388-22559402 chr20:22559384-22559398 chr20:22559383-22559397
46	POLR2A	chr20:22558382-22559736	PANC-1	pancreas:	n/a	n/a
47	SMC3	chr20:22559248-22559603	HepG2	liver:	n/a	n/a
48	EP300	chr20:22559024-22559614	HepG2	liver:	n/a	chr20:22559388-22559402 chr20:22559384-22559398 chr20:22559383-22559397
49	TEAD4	chr20:22558970-22559734	HepG2	liver:	n/a	n/a
50	JUND	chr20:22559246-22559682	A549	lung:	n/a	n/a

Variant related genes	Relation type
LINC00261	TF binding region

Extended variants
information (count: 37 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs1055080	0.82[CHD][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs11087387	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1203879	0.82[CEU][hapmap]
rs1203881	0.82[CEU][hapmap]
rs1203884	0.82[CEU][hapmap];0.94[TSI][hapmap]
rs1203892	0.80[EUR][1000 genomes]
rs1203894	0.80[EUR][1000 genomes]
rs1203905	0.87[CHD][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.84[ASN][1000 genomes]
rs1203907	0.87[CHD][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1209523	0.83[CHD][hapmap];1.00[JPT][hapmap]
rs1337918	0.85[ASN][1000 genomes]
rs1337919	1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap];0.85[ASN][1000 genomes]
rs1800847	0.83[ASN][1000 genomes]
rs1974	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2277762	0.84[EUR][1000 genomes]
rs2277763	0.84[EUR][1000 genomes]
rs2277764	0.85[ASN][1000 genomes]
rs2471	0.82[CEU][hapmap]
rs4815127	0.82[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.84[EUR][1000 genomes]
rs6036146	0.84[EUR][1000 genomes]
rs6036152	0.95[AFR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6048183	0.84[EUR][1000 genomes]
rs6048186	0.80[EUR][1000 genomes]
rs6048191	0.82[CEU][hapmap];0.84[EUR][1000 genomes]
rs6048192	0.84[EUR][1000 genomes]
rs6048196	0.82[CEU][hapmap];0.84[EUR][1000 genomes]
rs6048197	0.82[AFR][1000 genomes]
rs6048199	0.82[AFR][1000 genomes]
rs6048202	0.88[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs6048206	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6048209	1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap]
rs6113722	0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72470563	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73300991	0.81[ASN][1000 genomes]
rs73300993	0.81[ASN][1000 genomes]
rs932560	0.80[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv428690	chr20:22528757-22649625	Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Fasting glucose-related traits (interaction with BMI)	22581228	GWAS catalog

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:22555200-22560400	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
2	chr20:22556800-22560800	Active TSS	Pancreatic Islets	Pancreatic Islet
3	chr20:22557400-22560400	Active TSS	Pancreas	Pancrea
4	chr20:22558200-22560000	Bivalent Enhancer	Fetal Muscle Trunk	muscle
5	chr20:22558200-22560200	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr20:22558400-22560000	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr20:22558400-22560000	Bivalent Enhancer	Adipose Nuclei	Adipose
8	chr20:22558400-22560000	Bivalent/Poised TSS	Rectal Smooth Muscle	rectum
9	chr20:22558600-22559800	Bivalent/Poised TSS	Fetal Lung	lung
10	chr20:22558600-22560000	Bivalent Enhancer	Left Ventricle	heart
11	chr20:22558600-22560400	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr20:22558800-22559800	Bivalent Enhancer	Skeletal Muscle Female	skeletal muscle
13	chr20:22558800-22560000	Bivalent/Poised TSS	NHEK	skin
14	chr20:22559000-22560000	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
15	chr20:22559000-22560000	Bivalent Enhancer	Fetal Heart	heart
16	chr20:22559000-22560000	Bivalent/Poised TSS	Fetal Intestine Small	intestine
17	chr20:22559000-22560000	Bivalent Enhancer	Placenta Amnion	Placenta Amnion
18	chr20:22559000-22560000	Bivalent/Poised TSS	Rectal Mucosa Donor 29	rectum
19	chr20:22559000-22560200	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
20	chr20:22559200-22559800	Bivalent/Poised TSS	Colonic Mucosa	Colon
21	chr20:22559200-22560000	Bivalent/Poised TSS	Psoas Muscle	Psoas
22	chr20:22559200-22560600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr20:22559200-22562200	Weak transcription	Gastric	stomach
24	chr20:22559400-22559800	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
25	chr20:22559400-22559800	Bivalent/Poised TSS	Brain Substantia Nigra	brain
26	chr20:22559400-22559800	Active TSS	Stomach Mucosa	stomach
27	chr20:22559400-22560000	Flanking Bivalent TSS/Enh	Brain Hippocampus Middle	brain
28	chr20:22559400-22560000	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
29	chr20:22559400-22560000	Bivalent Enhancer	Placenta	Placenta
30	chr20:22559400-22560000	Flanking Bivalent TSS/Enh	Skeletal Muscle Male	skeletal muscle
31	chr20:22559400-22560000	Flanking Active TSS	HepG2	liver
32	chr20:22559400-22560000	Bivalent/Poised TSS	HMEC	breast
33	chr20:22559600-22559800	Flanking Bivalent TSS/Enh	HUES48 Cell Line	embryonic stem cell
34	chr20:22559600-22559800	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
35	chr20:22559600-22559800	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
36	chr20:22559600-22559800	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr20:22559600-22559800	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr20:22559600-22559800	Bivalent/Poised TSS	Fetal Stomach	stomach
39	chr20:22559600-22560000	Bivalent Enhancer	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr20:22559600-22560000	Flanking Bivalent TSS/Enh	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr20:22559600-22560000	Bivalent/Poised TSS	Primary T cells from cord blood	blood
42	chr20:22559600-22560000	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr20:22559600-22560000	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr20:22559600-22560000	Flanking Active TSS	Liver	Liver
45	chr20:22559600-22560000	Bivalent Enhancer	Brain Cingulate Gyrus	brain
46	chr20:22559600-22560000	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
47	chr20:22559600-22560000	Bivalent Enhancer	Fetal Muscle Leg	muscle
48	chr20:22559600-22560000	Flanking Bivalent TSS/Enh	Rectal Mucosa Donor 31	rectum
49	chr20:22559600-22560000	Flanking Bivalent TSS/Enh	Stomach Smooth Muscle	stomach
50	chr20:22559600-22560200	Flanking Active TSS	A549	lung

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