Variant report

Variant	rs7523560
Chromosome Location	chr1:149984306-149984307
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	EGR1	chr1:149984044-149984335	K562	blood:	n/a	chr1:149984182-149984204

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:149853005..149861438-chr1:149978765..149991065,34	MCF-7	breast:
2	chr1:149898259..149901942-chr1:149980885..149984493,5	MCF-7	breast:
3	chr1:149855536..149863300-chr1:149977462..149985642,29	K562	blood:
4	chr1:149977821..149984701-chr1:150037094..150041280,13	MCF-7	breast:
5	chr1:149854540..149863300-chr1:149979575..149985253,19	K562	blood:
6	chr1:149857288..149861878-chr1:149980292..149985449,12	MCF-7	breast:

No data

Variant related genes	Relation type
OTUD7B	TF binding region
ENSG00000143368	Chromatin interaction
ENSG00000184678	Chromatin interaction
ENSG00000136631	Chromatin interaction
ENSG00000184270	Chromatin interaction
ENSG00000184260	Chromatin interaction
ENSG00000178096	Chromatin interaction

Extended variants
information (count: 63 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs12059874	1.00[MEX][hapmap]
rs1556934	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs15916	0.83[AMR][1000 genomes]
rs16832989	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.91[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16832993	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16833048	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16836857	1.00[ASW][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs16837054	1.00[ASW][hapmap];1.00[MEX][hapmap];1.00[AMR][1000 genomes]
rs16837367	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16837593	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16838449	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16838646	1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16841141	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16841623	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16841697	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56929499	1.00[AMR][1000 genomes]
rs57020352	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57182882	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57513077	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58100431	1.00[AMR][1000 genomes]
rs58137104	0.83[AMR][1000 genomes]
rs58688107	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58777569	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59462540	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59709800	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59934949	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60631776	1.00[AMR][1000 genomes]
rs6664973	1.00[AMR][1000 genomes]
rs6680574	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6694482	1.00[ASW][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6700399	0.91[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73004328	1.00[AMR][1000 genomes]
rs73004398	1.00[AMR][1000 genomes]
rs73004400	1.00[AMR][1000 genomes]
rs73006303	1.00[AMR][1000 genomes]
rs73006306	1.00[AMR][1000 genomes]
rs73006313	1.00[AMR][1000 genomes]
rs73006316	1.00[AMR][1000 genomes]
rs73006318	1.00[AMR][1000 genomes]
rs73006327	1.00[AMR][1000 genomes]
rs73006333	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73008163	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73008167	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73008171	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73008191	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73008199	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73008201	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73010104	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73010113	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73010183	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73010186	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73010189	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73011904	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73011906	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73011909	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73011910	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73011912	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73011913	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73011915	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73011930	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs73016112	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7543861	1.00[AFR][1000 genomes];1.00[AMR][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	nsv831537	chr1:149833357-150064655	Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	431 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:149982800-149994400	Weak transcription	Gastric	stomach
2	chr1:149983000-149985600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr1:149983000-149992800	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr1:149983200-149984600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr1:149983200-149984800	Enhancers	Brain Substantia Nigra	brain
6	chr1:149983200-149984800	Enhancers	Osteobl	bone
7	chr1:149983200-149985000	Enhancers	Muscle Satellite Cultured Cells	--
8	chr1:149983200-149985000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr1:149983200-149985000	Enhancers	Hela-S3	cervix
10	chr1:149983200-149985200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr1:149983200-149985200	Enhancers	Rectal Mucosa Donor 31	rectum
12	chr1:149983200-149985200	Enhancers	Stomach Mucosa	stomach
13	chr1:149983200-149985400	Enhancers	HSMM	muscle
14	chr1:149983200-149985600	Enhancers	Fetal Intestine Small	intestine
15	chr1:149983200-149987400	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr1:149983200-149987600	Weak transcription	Right Atrium	heart
17	chr1:149983400-149984400	Weak transcription	Cortex derived primary cultured neurospheres	brain
18	chr1:149983400-149984600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr1:149983400-149984600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr1:149983400-149984600	Weak transcription	Duodenum Mucosa	Duodenum
21	chr1:149983400-149984600	Weak transcription	Fetal Intestine Large	intestine
22	chr1:149983400-149984800	Weak transcription	Adipose Nuclei	Adipose
23	chr1:149983400-149984800	Enhancers	Brain Hippocampus Middle	brain
24	chr1:149983400-149984800	Weak transcription	GM12878-XiMat	blood
25	chr1:149983400-149985000	Enhancers	K562	blood
26	chr1:149983400-149985000	Weak transcription	NH-A	brain
27	chr1:149983400-149985200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr1:149983400-149985400	Enhancers	Brain Angular Gyrus	brain
29	chr1:149983400-149985400	Enhancers	Brain Cingulate Gyrus	brain
30	chr1:149983400-149985400	Enhancers	Brain Inferior Temporal Lobe	brain
31	chr1:149983400-149985400	Enhancers	HepG2	liver
32	chr1:149983400-149987600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
33	chr1:149983400-149988800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr1:149983400-149988800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
35	chr1:149983400-149989000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr1:149983400-149989400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr1:149983400-149989400	Weak transcription	Skeletal Muscle Female	skeletal muscle
38	chr1:149983600-149984400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr1:149983600-149984800	Weak transcription	Liver	Liver
40	chr1:149983600-149984800	Weak transcription	Rectal Mucosa Donor 29	rectum
41	chr1:149983600-149985000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr1:149983600-149987600	Weak transcription	A549	lung
43	chr1:149983800-149984800	Enhancers	Brain Anterior Caudate	brain
44	chr1:149983800-149985200	Enhancers	HSMMtube	muscle
45	chr1:149984000-149984600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr1:149984000-149984600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr1:149984200-149985000	Enhancers	Colonic Mucosa	Colon

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links