Variant report

Variant	rs28710392
Chromosome Location	chr2:179381987-179381988
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:179377244..179379642-chr2:179381924..179384722,3	K562	blood:
2	chr2:179362528..179364837-chr2:179381836..179383554,2	K562	blood:
3	chr2:179381119..179383351-chr2:179385960..179387910,2	MCF-7	breast:
4	chr2:179370789..179373251-chr2:179379884..179382133,2	MCF-7	breast:
5	chr2:179379711..179384149-chr2:179385113..179390649,7	K562	blood:

Variant related genes	Relation type
ENSG00000237298	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10164753	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10497517	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11897366	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16866416	0.81[AMR][1000 genomes]
rs28560297	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28653157	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4894023	1.00[ASN][1000 genomes]
rs4894025	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4894027	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4894028	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62621236	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6710877	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6732060	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6735083	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs747122	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9808036	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv834467	chr2:179258140-179430965	Active TSS Strong transcription Flanking Active TSS Enhancers Weak transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
2	nsv834468	chr2:179351116-179533625	Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:179346400-179387800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr2:179350400-179384400	Strong transcription	Monocytes-CD14+_RO01746	blood
3	chr2:179359400-179382800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr2:179359600-179387600	Weak transcription	Right Ventricle	heart
5	chr2:179359600-179387800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr2:179360600-179382400	Weak transcription	Gastric	stomach
7	chr2:179360600-179383200	Weak transcription	Pancreas	Pancrea
8	chr2:179360800-179383000	Weak transcription	Aorta	Aorta
9	chr2:179360800-179387800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr2:179361000-179387800	Weak transcription	Spleen	Spleen
11	chr2:179361400-179387200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr2:179364600-179382800	Weak transcription	Thymus	Thymus
13	chr2:179365000-179383000	Weak transcription	Lung	lung
14	chr2:179365600-179387800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr2:179366000-179387600	Weak transcription	Fetal Brain Male	brain
16	chr2:179366000-179387800	Weak transcription	Small Intestine	intestine
17	chr2:179367400-179383200	Weak transcription	NHLF	lung
18	chr2:179367600-179387600	Weak transcription	Fetal Kidney	kidney
19	chr2:179367800-179387600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
20	chr2:179368000-179383000	Weak transcription	Ovary	ovary
21	chr2:179368200-179382400	Weak transcription	Brain Germinal Matrix	brain
22	chr2:179368200-179387600	Weak transcription	Fetal Heart	heart
23	chr2:179368200-179387600	Weak transcription	Fetal Lung	lung
24	chr2:179368200-179387800	Weak transcription	Brain Substantia Nigra	brain
25	chr2:179368400-179383000	Weak transcription	Placenta Amnion	Placenta Amnion
26	chr2:179368400-179383400	Weak transcription	Brain Angular Gyrus	brain
27	chr2:179368400-179387400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
28	chr2:179368400-179387600	Weak transcription	Skeletal Muscle Male	skeletal muscle
29	chr2:179368600-179382400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr2:179368600-179382600	Weak transcription	Brain Cingulate Gyrus	brain
31	chr2:179368600-179383000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
32	chr2:179368600-179387400	Weak transcription	A549	lung
33	chr2:179368600-179387600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr2:179368600-179387800	Weak transcription	Psoas Muscle	Psoas
35	chr2:179369000-179387400	Weak transcription	Colon Smooth Muscle	Colon
36	chr2:179369200-179387400	Weak transcription	K562	blood
37	chr2:179369200-179387600	Weak transcription	HUVEC	blood vessel
38	chr2:179369600-179382200	Weak transcription	Stomach Smooth Muscle	stomach
39	chr2:179369800-179382400	Weak transcription	Brain Hippocampus Middle	brain
40	chr2:179370200-179382600	Weak transcription	Skeletal Muscle Female	skeletal muscle
41	chr2:179370600-179387600	Weak transcription	Fetal Thymus	thymus
42	chr2:179371600-179387400	Weak transcription	HepG2	liver
43	chr2:179371600-179387600	Weak transcription	Rectal Mucosa Donor 31	rectum
44	chr2:179372200-179382400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr2:179372600-179387600	Weak transcription	HUES6 Cell Line	embryonic stem cell
46	chr2:179372800-179387800	Weak transcription	HUES64 Cell Line	embryonic stem cell
47	chr2:179373600-179388000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
48	chr2:179373800-179382400	Weak transcription	Fetal Brain Female	brain
49	chr2:179374000-179386600	Weak transcription	Primary neutrophils fromperipheralblood	blood
50	chr2:179374600-179382200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links