Variant report

Variant	rs278124
Chromosome Location	chr12:120129431-120129432
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:120126910..120129886-chr12:120131473..120133704,2	K562	blood:
2	chr12:120122749..120126442-chr12:120127143..120130647,6	K562	blood:
3	chr12:120128257..120130675-chr12:120137336..120140056,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000255692	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10774512	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1123790	0.89[EUR][1000 genomes]
rs12309592	0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1318272	0.81[JPT][hapmap]
rs175879	0.81[JPT][hapmap]
rs1985793	0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs202985	0.81[JPT][hapmap]
rs203327	1.00[ASW][hapmap]
rs2188711	0.89[EUR][1000 genomes]
rs2301655	0.93[CEU][hapmap];0.92[GIH][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes]
rs2393549	0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2393550	0.86[CHB][hapmap];0.95[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.84[ASN][1000 genomes]
rs2519536	0.87[CEU][hapmap]
rs278128	0.81[JPT][hapmap]
rs278129	0.81[JPT][hapmap]
rs278130	0.83[CEU][hapmap];0.81[JPT][hapmap];0.94[TSI][hapmap]
rs278131	0.81[JPT][hapmap]
rs278135	0.81[JPT][hapmap]
rs2893806	0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3213626	0.81[JPT][hapmap]
rs4766946	0.81[JPT][hapmap]
rs4767836	0.82[EUR][1000 genomes]
rs4767838	0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6490263	0.84[EUR][1000 genomes]
rs6490264	0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6490265	0.86[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs7953776	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7969977	0.92[EUR][1000 genomes]
rs904654	0.86[JPT][hapmap]
rs904655	0.81[JPT][hapmap]

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	nsv1052595	chr12:119992580-120132038	Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
2	nsv541616	chr12:119992580-120132038	Weak transcription Enhancers Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs278124	P2RX7	cis	parietal	SCAN
rs278124	PRKAB1	cis	cerebellum	SCAN

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:120108200-120161000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr12:120112600-120130400	Weak transcription	Right Atrium	heart
3	chr12:120116800-120201800	Weak transcription	Fetal Heart	heart
4	chr12:120117000-120145800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr12:120119200-120130200	Weak transcription	Brain Angular Gyrus	brain
6	chr12:120119200-120135400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr12:120119200-120141200	Weak transcription	Rectal Smooth Muscle	rectum
8	chr12:120119600-120130200	Weak transcription	Colon Smooth Muscle	Colon
9	chr12:120119600-120147000	Weak transcription	Brain Substantia Nigra	brain
10	chr12:120119800-120149800	Weak transcription	Placenta	Placenta
11	chr12:120120000-120129600	Weak transcription	Brain Hippocampus Middle	brain
12	chr12:120120000-120135000	Weak transcription	Esophagus	oesophagus
13	chr12:120120000-120135200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr12:120120200-120148000	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr12:120120400-120130200	Weak transcription	Brain Cingulate Gyrus	brain
16	chr12:120120400-120137200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
17	chr12:120120400-120145600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr12:120120800-120137600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr12:120121000-120151800	Weak transcription	Primary T cells from cord blood	blood
20	chr12:120121200-120173400	Weak transcription	Primary B cells from cord blood	blood
21	chr12:120121400-120130400	Weak transcription	NH-A	brain
22	chr12:120122200-120130200	Weak transcription	Duodenum Smooth Muscle	Duodenum
23	chr12:120122200-120160800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
24	chr12:120123400-120136200	Strong transcription	Thymus	Thymus
25	chr12:120123400-120182000	Strong transcription	Dnd41	blood
26	chr12:120123600-120130400	Weak transcription	Psoas Muscle	Psoas
27	chr12:120123600-120132200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
28	chr12:120124200-120131200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr12:120124200-120132400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr12:120124400-120130200	Weak transcription	Ovary	ovary
31	chr12:120125400-120129600	Strong transcription	Hela-S3	cervix
32	chr12:120125400-120130400	Weak transcription	Pancreas	Pancrea
33	chr12:120125400-120131600	Strong transcription	GM12878-XiMat	blood
34	chr12:120125400-120134800	Weak transcription	Gastric	stomach
35	chr12:120125600-120130000	Weak transcription	Muscle Satellite Cultured Cells	--
36	chr12:120125800-120134800	Weak transcription	HMEC	breast
37	chr12:120126000-120154000	Weak transcription	Right Ventricle	heart
38	chr12:120126200-120130200	Weak transcription	Adipose Nuclei	Adipose
39	chr12:120126400-120129600	Weak transcription	NHLF	lung
40	chr12:120126400-120134600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
41	chr12:120126400-120150000	Weak transcription	Primary hematopoietic stem cells	blood
42	chr12:120126600-120129800	Weak transcription	Fetal Brain Female	brain
43	chr12:120126600-120134400	Weak transcription	H9 Cell Line	embryonic stem cell
44	chr12:120126600-120158000	Weak transcription	Colonic Mucosa	Colon
45	chr12:120126800-120135400	Weak transcription	NHEK	skin
46	chr12:120127600-120130600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr12:120127600-120143200	Strong transcription	Monocytes-CD14+_RO01746	blood
48	chr12:120128400-120130200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
49	chr12:120128400-120130200	Enhancers	Rectal Mucosa Donor 29	rectum
50	chr12:120128400-120131000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links