Variant report

Variant	rs2523750
Chromosome Location	chr6:30228416-30228417
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:30225449..30228967-chr6:30292795..30296377,4	K562	blood:
2	chr6:30226682..30228906-chr6:30311932..30314057,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000231074	Chromatin interaction
ENSG00000241370	Chromatin interaction
ENSG00000270604	Chromatin interaction
ENSG00000204599	Chromatin interaction

Extended variants
information (count: 63 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs1045251	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1060065	0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1264616	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1473102	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2023476	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2023477	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2023478	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2057727	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2074474	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2097773	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2394779	0.80[ASN][1000 genomes]
rs2394780	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2508026	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2516697	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2516699	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2516700	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2516701	0.86[AFR][1000 genomes]
rs2516702	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2516704	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2516705	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2516706	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2516707	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2516710	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2516713	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2516718	0.90[AFR][1000 genomes]
rs2516719	0.89[AFR][1000 genomes]
rs2523737	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2523744	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2523745	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2523746	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2523747	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2523748	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs261943	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs261948	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs261949	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28360021	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28360023	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2844752	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2844761	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2844763	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2844765	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3778624	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6912239	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6912495	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7452694	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7767817	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9295843	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9295844	0.81[ASN][1000 genomes]
rs9357095	0.80[ASN][1000 genomes]
rs9368628	0.80[ASN][1000 genomes]
rs9368632	0.80[ASN][1000 genomes]
rs9368633	0.80[ASN][1000 genomes]
rs9380168	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9380174	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9391679	0.80[ASN][1000 genomes]
rs9391806	0.80[ASN][1000 genomes]
rs9391807	0.80[ASN][1000 genomes]
rs9393999	0.80[ASN][1000 genomes]
rs9394000	0.80[ASN][1000 genomes]
rs9394001	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9394003	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs962899	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs974963	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2523750	HCG18	cis	normal skin	skin_eQTL
rs2523750	LOC401245	cis	multi-tissue	Pritchard
rs2523750	TRIM26	Cis_1M	lymphoblastoid	RTeQTL
rs2523750	HCG18	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:78 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:30226600-30229000	Active TSS	Brain Inferior Temporal Lobe	brain
2	chr6:30226800-30228600	Enhancers	Fetal Brain Male	brain
3	chr6:30226800-30228600	Enhancers	Fetal Heart	heart
4	chr6:30226800-30228800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr6:30227200-30228600	Active TSS	Primary T cells from cord blood	blood
6	chr6:30227200-30228800	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
7	chr6:30227200-30228800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr6:30227200-30228800	Active TSS	Rectal Mucosa Donor 31	rectum
9	chr6:30227200-30228800	Active TSS	Osteobl	bone
10	chr6:30227400-30228600	Active TSS	Hela-S3	cervix
11	chr6:30227800-30228600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
12	chr6:30227800-30228600	Flanking Active TSS	Stomach Smooth Muscle	stomach
13	chr6:30227800-30228600	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
14	chr6:30227800-30228800	Flanking Active TSS	Adipose Nuclei	Adipose
15	chr6:30228000-30228600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
16	chr6:30228000-30228800	Flanking Active TSS	Right Ventricle	heart
17	chr6:30228000-30229800	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr6:30228200-30228600	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
19	chr6:30228200-30228600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
20	chr6:30228200-30228600	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
21	chr6:30228200-30228600	Flanking Bivalent TSS/Enh	Primary T helper cells fromperipheralblood	blood
22	chr6:30228200-30228600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
23	chr6:30228200-30228600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr6:30228200-30228600	Flanking Active TSS	Brain Anterior Caudate	brain
25	chr6:30228200-30228600	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
26	chr6:30228200-30228600	Flanking Active TSS	Fetal Brain Female	brain
27	chr6:30228200-30228600	Enhancers	Pancreas	Pancrea
28	chr6:30228200-30228600	Flanking Active TSS	GM12878-XiMat	blood
29	chr6:30228200-30228800	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
30	chr6:30228200-30228800	Bivalent/Poised TSS	Primary neutrophils fromperipheralblood	blood
31	chr6:30228200-30228800	Enhancers	Primary T helper naive cells from peripheral blood	blood
32	chr6:30228200-30228800	Enhancers	Lung	lung
33	chr6:30228200-30229400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
34	chr6:30228200-30231200	Weak transcription	Ovary	ovary
35	chr6:30228200-30232000	Weak transcription	HSMMtube	muscle
36	chr6:30228200-30234200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr6:30228200-30237400	Weak transcription	Aorta	Aorta
38	chr6:30228400-30228600	Bivalent Enhancer	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr6:30228400-30228600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr6:30228400-30228600	Bivalent/Poised TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr6:30228400-30228600	Enhancers	Cortex derived primary cultured neurospheres	brain
42	chr6:30228400-30228600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr6:30228400-30228600	Enhancers	Brain Substantia Nigra	brain
44	chr6:30228400-30228600	Weak transcription	Duodenum Smooth Muscle	Duodenum
45	chr6:30228400-30228600	Bivalent Enhancer	Fetal Muscle Trunk	muscle
46	chr6:30228400-30228600	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
47	chr6:30228400-30228600	Bivalent Enhancer	Stomach Mucosa	stomach
48	chr6:30228400-30228800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr6:30228400-30228800	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell
50	chr6:30228400-30228800	Enhancers	Primary T cells fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links