Variant report

Variant	rs55974181
Chromosome Location	chr2:172294813-172294814
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:172288399..172297381-chr2:172370978..172381493,22	K562	blood:
2	chr2:172294486..172297106-chr2:172372290..172374923,2	K562	blood:
3	chr2:172012919..172015830-chr2:172294656..172296953,2	K562	blood:
4	chr2:172016933..172018793-chr2:172293106..172294820,2	MCF-7	breast:
5	chr2:172287467..172293160-chr2:172293206..172300397,21	K562	blood:

Variant related genes	Relation type
ENSG00000123600	Chromatin interaction
ENSG00000115827	Chromatin interaction
ENSG00000071967	Chromatin interaction
ENSG00000233762	Chromatin interaction
ENSG00000198586	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs16859368	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16859371	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16859373	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16859377	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16859380	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16859386	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16859390	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs16859404	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs16859405	0.96[EUR][1000 genomes]
rs16859410	0.96[EUR][1000 genomes]
rs1882378	0.96[EUR][1000 genomes]
rs3731984	0.96[EUR][1000 genomes]
rs3795996	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs55711751	0.88[EUR][1000 genomes]
rs55715902	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55716501	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs56065525	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56239048	0.85[EUR][1000 genomes]
rs56273218	0.81[EUR][1000 genomes]
rs56302833	0.88[EUR][1000 genomes]
rs57165050	0.88[EUR][1000 genomes]
rs61021737	0.88[EUR][1000 genomes]
rs61502503	0.88[EUR][1000 genomes]
rs728651	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73021048	0.88[EUR][1000 genomes]
rs73976175	0.92[EUR][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	esv3382346	chr2:172062677-172363892	Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
2	esv3349868	chr2:172276494-172302401	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	22 gene(s)	inside rSNPs	diseases
3	esv1832950	chr2:172283513-172488111	Flanking Active TSS Strong transcription Weak transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 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	chr2:172291000-172319800	Weak transcription	Stomach Mucosa	stomach
2	chr2:172291400-172295200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr2:172291400-172296200	Weak transcription	Lung	lung
4	chr2:172291400-172296200	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr2:172291400-172296200	Weak transcription	Spleen	Spleen
6	chr2:172291400-172296400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr2:172291400-172296400	Weak transcription	Aorta	Aorta
8	chr2:172291400-172296400	Weak transcription	Small Intestine	intestine
9	chr2:172291400-172297800	Weak transcription	Esophagus	oesophagus
10	chr2:172291400-172297800	Weak transcription	Gastric	stomach
11	chr2:172291600-172295200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr2:172291600-172295200	Weak transcription	Fetal Muscle Trunk	muscle
13	chr2:172291600-172295200	Weak transcription	Ovary	ovary
14	chr2:172291600-172296000	Weak transcription	Right Ventricle	heart
15	chr2:172291600-172297800	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr2:172291600-172304000	Weak transcription	Pancreas	Pancrea
17	chr2:172291600-172305200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr2:172291600-172311800	Weak transcription	Fetal Brain Male	brain
19	chr2:172291800-172295000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr2:172291800-172295200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr2:172291800-172295200	Weak transcription	Fetal Stomach	stomach
22	chr2:172291800-172296400	Weak transcription	Brain Germinal Matrix	brain
23	chr2:172291800-172296400	Weak transcription	Colonic Mucosa	Colon
24	chr2:172291800-172296600	Weak transcription	H9 Cell Line	embryonic stem cell
25	chr2:172291800-172297800	Weak transcription	HSMMtube	muscle
26	chr2:172291800-172300000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
27	chr2:172291800-172306400	Weak transcription	Psoas Muscle	Psoas
28	chr2:172291800-172338200	Weak transcription	Primary neutrophils fromperipheralblood	blood
29	chr2:172292000-172295200	Weak transcription	Cortex derived primary cultured neurospheres	brain
30	chr2:172292000-172296000	Weak transcription	Thymus	Thymus
31	chr2:172292000-172296400	Weak transcription	Stomach Smooth Muscle	stomach
32	chr2:172292000-172297200	Weak transcription	NHLF	lung
33	chr2:172292000-172304400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
34	chr2:172292000-172312800	Weak transcription	Pancreatic Islets	Pancreatic Islet
35	chr2:172292000-172341600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
36	chr2:172292200-172295200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
37	chr2:172292200-172295400	Weak transcription	Fetal Heart	heart
38	chr2:172292200-172297400	Weak transcription	Hela-S3	cervix
39	chr2:172292400-172295200	Strong transcription	Skeletal Muscle Female	skeletal muscle
40	chr2:172292400-172296000	Weak transcription	Fetal Brain Female	brain
41	chr2:172292400-172296200	Weak transcription	Rectal Smooth Muscle	rectum
42	chr2:172292400-172298600	Strong transcription	H1 Cell Line	embryonic stem cell
43	chr2:172292400-172299400	Strong transcription	Fetal Muscle Leg	muscle
44	chr2:172292400-172301200	Strong transcription	Placenta	Placenta
45	chr2:172292400-172301800	Strong transcription	HUES48 Cell Line	embryonic stem cell
46	chr2:172292600-172295000	Genic enhancers	Dnd41	blood
47	chr2:172292600-172295200	Weak transcription	Fetal Intestine Small	intestine
48	chr2:172292600-172295200	Strong transcription	Skeletal Muscle Male	skeletal muscle
49	chr2:172292600-172295800	Strong transcription	Brain Cingulate Gyrus	brain
50	chr2:172292600-172297000	Weak transcription	Brain Substantia Nigra	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links