Variant report

Variant	rs10199055
Chromosome Location	chr2:20426090-20426091
allele	A/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	CTCF	chr2:20426090-20426465	MCF-7	breast:	n/a	n/a
2	RAD21	chr2:20420269-20426598	SK-N-SH	brain:	n/a	chr2:20422198-20422210 chr2:20424162-20424172 chr2:20425226-20425238 chr2:20423347-20423361
3	ESRRA	chr2:20424274-20426108	GM12878	blood:	n/a	chr2:20425299-20425312 chr2:20425885-20425901
4	ZNF263	chr2:20424394-20426249	HEK293-T-REx	kidney:	n/a	n/a
5	MAX	chr2:20422503-20426249	HepG2	liver:	n/a	chr2:20423191-20423198 chr2:20424483-20424490 chr2:20423189-20423200 chr2:20424338-20424348 chr2:20423190-20423199 chr2:20423540-20423550 chr2:20423190-20423200 chr2:20424526-20424536 chr2:20423189-20423199
6	CTCF	chr2:20426040-20426190	A549	lung:	n/a	n/a
7	CTCF	chr2:20426020-20426170	HBMEC	blood vessel:	n/a	n/a
8	MYBL2	chr2:20424431-20426143	HepG2	liver:	n/a	n/a
9	MAX	chr2:20424979-20426145	H1-hESC	embryonic stem cell:	n/a	n/a
10	E2F6	chr2:20424981-20426097	H1-hESC	embryonic stem cell:	n/a	chr2:20425402-20425411
11	MBD4	chr2:20424987-20426304	HepG2	liver:	n/a	n/a
12	CTCF	chr2:20426065-20426537	HCT-116	colon:	n/a	n/a
13	MAX	chr2:20424290-20426109	H1-hESC	embryonic stem cell:	n/a	chr2:20424483-20424490 chr2:20424338-20424348 chr2:20424526-20424536
14	YY1	chr2:20425023-20426205	H1-hESC	embryonic stem cell:	n/a	chr2:20425836-20425844 chr2:20425825-20425847 chr2:20425301-20425312
15	CTCF	chr2:20421105-20426546	SK-N-SH	brain:	n/a	chr2:20425315-20425325 chr2:20423923-20423936
16	YY1	chr2:20424958-20426180	HepG2	liver:	n/a	chr2:20425836-20425844 chr2:20425825-20425847 chr2:20425301-20425312
17	RAD21	chr2:20426052-20426491	MCF-7	breast:	n/a	n/a
18	MAX	chr2:20422636-20426156	HepG2	liver:	n/a	chr2:20423191-20423198 chr2:20424483-20424490 chr2:20423189-20423200 chr2:20424338-20424348 chr2:20423190-20423199 chr2:20423540-20423550 chr2:20423190-20423200 chr2:20424526-20424536 chr2:20423189-20423199
19	E2F6	chr2:20424954-20426207	H1-hESC	embryonic stem cell:	n/a	chr2:20425402-20425411

No.	Distal block	Cell Line	Cell type
1	chr2:20299695..20307724-chr2:20421846..20426859,15	MCF-7	breast:
2	chr2:20425705..20426396-chr2:20447809..20448700,2	MCF-7	breast:
3	chr2:20424066..20426931-chr2:20646792..20649592,2	MCF-7	breast:
4	chr2:20425935..20426603-chr2:20441699..20442616,3	MCF-7	breast:
5	chr2:20421499..20423791-chr2:20425335..20427623,2	K562	blood:

Variant related genes	Relation type
SDC1	TF binding region
ENSG00000143878	Chromatin interaction
ENSG00000115884	Chromatin interaction
ENSG00000234378	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10166227	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10171976	0.87[EUR][1000 genomes]
rs10183906	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10206812	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13429586	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3771249	1.00[ASN][1000 genomes]
rs57065686	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs59231157	0.82[EUR][1000 genomes]
rs62109732	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62109734	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62109735	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62109736	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62109737	1.00[EUR][1000 genomes]
rs62111435	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs62111436	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9808229	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1846803	chr2:20409322-20427189	Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	diseases
2	esv1798036	chr2:20423264-20442631	Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	esv1846193	chr2:20423264-20442631	Bivalent/Poised TSS Enhancers Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	esv1849406	chr2:20423264-20442631	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	esv1819683	chr2:20423264-20455467	Active TSS Bivalent/Poised TSS Weak transcription Flanking Active TSS Strong transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
6	esv3398925	chr2:20423871-20426119	Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:20425200-20426200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr2:20425200-20426200	Flanking Active TSS	Colonic Mucosa	Colon
3	chr2:20425400-20426200	Bivalent Enhancer	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr2:20425400-20426200	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr2:20425400-20426200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr2:20425400-20426200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr2:20425400-20426200	Flanking Active TSS	Liver	Liver
8	chr2:20425400-20426200	Enhancers	Gastric	stomach
9	chr2:20425400-20426200	Enhancers	Pancreas	Pancrea
10	chr2:20425400-20426200	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
11	chr2:20425400-20426200	Enhancers	Sigmoid Colon	Sigmoid Colon
12	chr2:20425400-20426200	Flanking Active TSS	HepG2	liver
13	chr2:20425600-20426200	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
14	chr2:20425600-20426200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr2:20425600-20426200	Enhancers	Fetal Lung	lung
16	chr2:20425600-20426200	Enhancers	Placenta Amnion	Placenta Amnion
17	chr2:20425600-20426200	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
18	chr2:20425600-20426400	Bivalent Enhancer	Placenta	Placenta
19	chr2:20425600-20426400	Enhancers	Stomach Mucosa	stomach
20	chr2:20425600-20427800	Weak transcription	Osteobl	bone
21	chr2:20425600-20429400	Weak transcription	NHDF-Ad	bronchial
22	chr2:20425600-20429800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr2:20425800-20426200	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
24	chr2:20425800-20426200	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
25	chr2:20425800-20426200	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
26	chr2:20425800-20426200	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
27	chr2:20425800-20426200	Enhancers	Breast Myoepithelial Primary Cells	Breast
28	chr2:20425800-20426200	Bivalent Enhancer	Fetal Muscle Trunk	muscle
29	chr2:20425800-20426200	Bivalent Enhancer	Fetal Muscle Leg	muscle
30	chr2:20425800-20426200	Bivalent Enhancer	Fetal Stomach	stomach
31	chr2:20425800-20426200	Bivalent Enhancer	Thymus	Thymus
32	chr2:20425800-20426200	Enhancers	A549	lung
33	chr2:20425800-20426400	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
34	chr2:20425800-20426400	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell
35	chr2:20425800-20426400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
36	chr2:20425800-20426400	Enhancers	Esophagus	oesophagus
37	chr2:20425800-20426400	Enhancers	Fetal Intestine Large	intestine
38	chr2:20425800-20426400	Enhancers	Rectal Mucosa Donor 31	rectum
39	chr2:20425800-20426400	Enhancers	NHEK	skin
40	chr2:20425800-20427800	Enhancers	HMEC	breast
41	chr2:20425800-20431000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
42	chr2:20425800-20431000	Weak transcription	NH-A	brain
43	chr2:20426000-20426200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr2:20426000-20426200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr2:20426000-20426200	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr2:20426000-20426200	Enhancers	Duodenum Mucosa	Duodenum
47	chr2:20426000-20426200	Enhancers	Small Intestine	intestine
48	chr2:20426000-20426400	Enhancers	Fetal Intestine Small	intestine
49	chr2:20426000-20427600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr2:20426000-20430600	Weak transcription	Hela-S3	cervix

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