Variant report

Variant	rs73579400
Chromosome Location	chr20:1307777-1307778
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	NR3C1	chr20:1307697-1308261	A549	lung:	n/a	chr20:1307902-1307909 chr20:1307964-1307978 chr20:1307962-1307980 chr20:1307963-1307979 chr20:1307963-1307979 chr20:1307963-1307979 chr20:1307963-1307979 chr20:1307964-1307978 chr20:1307960-1307981
2	RAD21	chr20:1307712-1308342	IMR90	lung:	n/a	n/a
3	POLR2A	chr20:1305605-1310547	SK-N-MC	brain:	n/a	n/a
4	POLR2A	chr20:1307095-1307865	PFSK-1	brain:	n/a	n/a
5	POLR2A	chr20:1305513-1308378	GM12878	blood:	n/a	n/a
6	MYC	chr20:1305203-1307799	A549	lung:	n/a	n/a
7	POLR2A	chr20:1303332-1311264	MCF10A-Er-Src	breast:	n/a	n/a
8	POLR2A	chr20:1305735-1309277	HepG2	liver:	n/a	n/a
9	POLR2A	chr20:1304494-1308746	HUVEC	blood vessel:	n/a	n/a
10	POLR2A	chr20:1305703-1309289	HepG2	liver:	n/a	n/a
11	POLR2A	chr20:1305666-1312369	K562	blood:	n/a	n/a
12	POLR2A	chr20:1305676-1307857	K562	blood:	n/a	n/a
13	POLR2A	chr20:1304572-1308368	HUVEC	blood vessel:	n/a	n/a
14	POLR2A	chr20:1305442-1308085	H1-hESC	embryonic stem cell:	n/a	n/a
15	POLR2A	chr20:1304690-1311690	MCF10A-Er-Src	breast:	n/a	n/a
16	POLR2A	chr20:1307771-1308216	GM12878	blood:	n/a	n/a
17	POLR2A	chr20:1307227-1307791	HepG2	liver:	n/a	n/a
18	POLR2A	chr20:1307478-1307784	K562	blood:	n/a	n/a
19	POLR2A	chr20:1305633-1307785	GM18505	blood:	n/a	n/a
20	CHD1	chr20:1304469-1308818	IMR90	lung:	n/a	n/a
21	POLR2A	chr20:1305691-1309130	A549	lung:	n/a	n/a
22	POLR2A	chr20:1305219-1310566	HepG2	liver:	n/a	n/a
23	POLR2A	chr20:1305545-1309383	HepG2	liver:	n/a	n/a
24	POLR2A	chr20:1302125-1308990	IMR90	lung:	n/a	n/a
25	POLR2A	chr20:1307721-1309217	GM12878	blood:	n/a	n/a
26	POLR2A	chr20:1305630-1309107	GM12878	blood:	n/a	n/a
27	POLR2A	chr20:1305543-1308333	GM12892	blood:	n/a	n/a
28	POLR2A	chr20:1305209-1309043	GM12891	blood:	n/a	n/a
29	NR3C1	chr20:1307710-1308221	A549	lung:	n/a	chr20:1307902-1307909 chr20:1307964-1307978 chr20:1307962-1307980 chr20:1307963-1307979 chr20:1307963-1307979 chr20:1307963-1307979 chr20:1307963-1307979 chr20:1307964-1307978 chr20:1307960-1307981
30	POLR2A	chr20:1303290-1308319	HUVEC	blood vessel:	n/a	n/a
31	NR3C1	chr20:1307770-1308103	A549	lung:	n/a	chr20:1307902-1307909 chr20:1307964-1307978 chr20:1307962-1307980 chr20:1307963-1307979 chr20:1307963-1307979 chr20:1307963-1307979 chr20:1307963-1307979 chr20:1307964-1307978 chr20:1307960-1307981
32	POLR2A	chr20:1307451-1308360	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr20:1268133..1270306-chr20:1306878..1308946,2	MCF-7	breast:
2	chr20:1307748..1310698-chr20:1356609..1358929,2	K562	blood:
3	chr20:1306609..1308717-chr20:1373062..1375701,3	MCF-7	breast:
4	chr20:1306989..1309625-chr20:1321543..1324213,2	MCF-7	breast:
5	chr20:1307620..1309289-chr20:1370365..1373331,2	K562	blood:
6	chr20:1304653..1308515-chr20:1369739..1375969,7	MCF-7	breast:
7	chr20:1293745..1297831-chr20:1304825..1308186,3	MCF-7	breast:
8	chr20:1306070..1308541-chr20:1446001..1448028,2	MCF-7	breast:
9	chr20:1306581..1308202-chr20:1321732..1323458,2	K562	blood:

Variant related genes	Relation type
SDCBP2	TF binding region
ENSG00000088833	Chromatin interaction
ENSG00000125775	Chromatin interaction
ENSG00000088832	Chromatin interaction

Extended variants
information (count: 8 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs57806058	0.89[AFR][1000 genomes]
rs6104943	0.81[AFR][1000 genomes]
rs6109511	0.81[AFR][1000 genomes]
rs6109522	0.81[AFR][1000 genomes]
rs73581215	0.80[AFR][1000 genomes];0.87[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1057939	chr20:824980-1316778	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	nsv1057097	chr20:1030940-1314265	Active TSS Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Enhancers Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
3	nsv912595	chr20:1283523-1313762	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 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	chr20:1306600-1307800	Flanking Active TSS	Adipose Nuclei	Adipose
2	chr20:1306600-1307800	Flanking Active TSS	Rectal Smooth Muscle	rectum
3	chr20:1306600-1307800	Enhancers	Small Intestine	intestine
4	chr20:1306600-1308200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr20:1306600-1308600	Flanking Active TSS	Osteobl	bone
6	chr20:1306600-1309200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
7	chr20:1306600-1309400	Flanking Active TSS	Stomach Mucosa	stomach
8	chr20:1306600-1309400	Flanking Active TSS	GM12878-XiMat	blood
9	chr20:1306600-1309600	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
10	chr20:1306600-1309800	Flanking Active TSS	Duodenum Mucosa	Duodenum
11	chr20:1306600-1309800	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
12	chr20:1306600-1310000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr20:1306600-1311000	Enhancers	Spleen	Spleen
14	chr20:1306800-1307800	Flanking Active TSS	Fetal Intestine Small	intestine
15	chr20:1306800-1307800	Flanking Active TSS	A549	lung
16	chr20:1306800-1308600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr20:1306800-1309000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr20:1306800-1311400	Enhancers	Lung	lung
19	chr20:1307000-1308000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr20:1307000-1308000	Enhancers	Fetal Stomach	stomach
21	chr20:1307000-1308000	Weak transcription	Ovary	ovary
22	chr20:1307000-1308000	Enhancers	Thymus	Thymus
23	chr20:1307000-1308200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
24	chr20:1307000-1308400	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
25	chr20:1307000-1308400	Transcr. at gene 5' and 3'	NHEK	skin
26	chr20:1307000-1308600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
27	chr20:1307000-1308600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr20:1307000-1308600	Enhancers	Primary T helper naive cells from peripheral blood	blood
29	chr20:1307000-1308600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
30	chr20:1307000-1308800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr20:1307000-1309000	Enhancers	Fetal Thymus	thymus
32	chr20:1307000-1309000	Enhancers	Pancreas	Pancrea
33	chr20:1307000-1309000	Enhancers	Sigmoid Colon	Sigmoid Colon
34	chr20:1307000-1309200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr20:1307000-1309200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
36	chr20:1307000-1309200	Flanking Active TSS	HepG2	liver
37	chr20:1307000-1310200	Enhancers	Placenta	Placenta
38	chr20:1307000-1310800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
39	chr20:1307000-1311800	Enhancers	Primary T cells fromperipheralblood	blood
40	chr20:1307000-1312000	Enhancers	Primary T helper cells fromperipheralblood	blood
41	chr20:1307000-1314400	Enhancers	Left Ventricle	heart
42	chr20:1307200-1307800	Transcr. at gene 5' and 3'	Dnd41	blood
43	chr20:1307200-1308000	Weak transcription	Fetal Muscle Trunk	muscle
44	chr20:1307200-1308200	Enhancers	H1 Cell Line	embryonic stem cell
45	chr20:1307200-1308200	Enhancers	Primary T killer memory cells from peripheral blood	blood
46	chr20:1307200-1308400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
47	chr20:1307200-1308800	Enhancers	Primary hematopoietic stem cells	blood
48	chr20:1307200-1308800	Enhancers	Fetal Heart	heart
49	chr20:1307200-1309400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
50	chr20:1307200-1309800	Genic enhancers	Cortex derived primary cultured neurospheres	brain

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