Variant report

Variant	rs72881938
Chromosome Location	chr2:172628752-172628753
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:19)
CpG islands
(count:0)
Chromatin interactive
region (count:1)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:19 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MBD4	chr2:172628638-172629293	HepG2	liver:	n/a	n/a
2	SMC3	chr2:172628701-172629257	HepG2	liver:	n/a	n/a
3	POLR2A	chr2:172628227-172629157	HepG2	liver:	n/a	n/a
4	POLR2A	chr2:172628526-172629127	A549	lung:	n/a	n/a
5	TEAD4	chr2:172628524-172629511	HepG2	liver:	n/a	n/a
6	FOXA1	chr2:172628706-172629649	HepG2	liver:	n/a	n/a
7	ARID3A	chr2:172628651-172629610	HepG2	liver:	n/a	n/a
8	FOXA2	chr2:172628547-172630336	HepG2	liver:	n/a	n/a
9	STAT3	chr2:172628744-172628944	MCF10A-Er-Src	breast:	n/a	n/a
10	CHD2	chr2:172628702-172629158	HepG2	liver:	n/a	n/a
11	SETDB1	chr2:172627977-172628753	U2OS	brain:	n/a	n/a
12	MYBL2	chr2:172628711-172629533	HepG2	liver:	n/a	n/a
13	NFIC	chr2:172628585-172629460	HepG2	liver:	n/a	n/a
14	POLR2A	chr2:172628477-172628812	HUVEC	blood vessel:	n/a	n/a
15	POLR2A	chr2:172628071-172628969	K562	blood:	n/a	n/a
16	HDAC2	chr2:172628722-172629230	HepG2	liver:	n/a	n/a
17	POLR2A	chr2:172628572-172629037	PANC-1	pancreas:	n/a	n/a
18	HNF4G	chr2:172628636-172629215	HepG2	liver:	n/a	n/a
19	POLR2A	chr2:172628741-172628802	HUVEC	blood vessel:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:172621958..172624550-chr2:172626505..172629129,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000228389	TF binding region

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs12053046	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12614709	0.98[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12619041	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12620126	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12622772	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12622895	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs17581361	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs17581439	0.83[EUR][1000 genomes]
rs17615262	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2176465	0.98[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3736499	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3765166	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3765167	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3770448	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3770449	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3770455	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3821093	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs55957712	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs56275355	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs57718990	0.91[AMR][1000 genomes]
rs57775770	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62182370	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs62182372	0.98[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs62182373	0.98[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs62182374	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs62182392	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs72885532	0.94[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs72885545	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs72889848	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7584258	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[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	nsv834457	chr2:172564939-172770901	Strong transcription Genic enhancers Enhancers Weak transcription Active TSS Flanking 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	14 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:172587800-172640800	Weak transcription	Psoas Muscle	Psoas
2	chr2:172593200-172645000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr2:172603000-172688400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
4	chr2:172604400-172641200	Weak transcription	Colon Smooth Muscle	Colon
5	chr2:172609600-172628800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
6	chr2:172610200-172651400	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr2:172618000-172639600	Weak transcription	Fetal Heart	heart
8	chr2:172618400-172639800	Weak transcription	Rectal Mucosa Donor 29	rectum
9	chr2:172618400-172641000	Weak transcription	Aorta	Aorta
10	chr2:172618800-172640800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr2:172619000-172630600	Weak transcription	Lung	lung
12	chr2:172619000-172638800	Weak transcription	Primary T cells from cord blood	blood
13	chr2:172619000-172641000	Weak transcription	Spleen	Spleen
14	chr2:172619200-172632400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
15	chr2:172619200-172634600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
16	chr2:172619200-172635000	Weak transcription	Skeletal Muscle Female	skeletal muscle
17	chr2:172619200-172635200	Weak transcription	A549	lung
18	chr2:172619200-172638600	Weak transcription	Stomach Smooth Muscle	stomach
19	chr2:172619200-172640800	Weak transcription	Rectal Smooth Muscle	rectum
20	chr2:172619200-172641000	Weak transcription	Thymus	Thymus
21	chr2:172619200-172641600	Weak transcription	Gastric	stomach
22	chr2:172619200-172641800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr2:172619600-172640200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr2:172620000-172634200	Weak transcription	Brain Cingulate Gyrus	brain
25	chr2:172620200-172630800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr2:172620200-172634600	Weak transcription	Brain Angular Gyrus	brain
27	chr2:172620200-172641400	Weak transcription	NHEK	skin
28	chr2:172620400-172638600	Weak transcription	Primary B cells from cord blood	blood
29	chr2:172620400-172638600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr2:172620400-172638600	Weak transcription	HSMM	muscle
31	chr2:172620400-172641000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr2:172620400-172641600	Weak transcription	HUVEC	blood vessel
33	chr2:172620400-172641800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr2:172620600-172640000	Weak transcription	Muscle Satellite Cultured Cells	--
35	chr2:172620800-172634600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr2:172620800-172634600	Weak transcription	Brain Hippocampus Middle	brain
37	chr2:172620800-172634800	Weak transcription	NHDF-Ad	bronchial
38	chr2:172620800-172639600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr2:172620800-172640600	Weak transcription	Left Ventricle	heart
40	chr2:172620800-172640800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr2:172621000-172634400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr2:172621000-172640000	Weak transcription	Osteobl	bone
43	chr2:172621000-172648000	Weak transcription	HSMMtube	muscle
44	chr2:172624400-172634600	Weak transcription	Duodenum Smooth Muscle	Duodenum
45	chr2:172624600-172634800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr2:172624600-172640200	Weak transcription	Right Ventricle	heart
47	chr2:172624600-172640200	Weak transcription	Skeletal Muscle Male	skeletal muscle
48	chr2:172625000-172634200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr2:172628200-172629800	Enhancers	HepG2	liver
50	chr2:172628600-172628800	Strong transcription	Brain Anterior Caudate	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links