Variant report

Variant	rs12565798
Chromosome Location	chr1:67027837-67027838
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 52 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10493411	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10789211	0.87[EUR][1000 genomes]
rs10889629	0.92[ASN][1000 genomes]
rs11208900	0.83[EUR][1000 genomes]
rs11208901	0.85[EUR][1000 genomes]
rs11208907	1.00[ASN][1000 genomes]
rs11208908	0.91[ASN][1000 genomes]
rs11208910	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11208916	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11208924	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11208929	0.87[EUR][1000 genomes]
rs11208930	0.86[EUR][1000 genomes]
rs1156618	0.92[ASN][1000 genomes]
rs12023176	0.82[ASN][1000 genomes]
rs12025668	0.86[EUR][1000 genomes]
rs12034344	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12039282	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12041930	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12046520	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12046904	0.86[EUR][1000 genomes]
rs12048885	0.86[EUR][1000 genomes]
rs12402181	0.87[EUR][1000 genomes]
rs12567556	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1373909	0.91[ASN][1000 genomes]
rs1445578	0.81[EUR][1000 genomes]
rs1445579	0.83[EUR][1000 genomes]
rs17129062	0.85[EUR][1000 genomes]
rs17129064	0.85[EUR][1000 genomes]
rs17129065	0.86[EUR][1000 genomes]
rs2312153	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3795531	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4655498	0.91[ASN][1000 genomes]
rs4655620	0.91[ASN][1000 genomes]
rs57941297	0.85[EUR][1000 genomes]
rs6588209	0.87[EUR][1000 genomes]
rs6680968	0.91[ASN][1000 genomes]
rs6687137	0.91[ASN][1000 genomes]
rs6697068	0.86[EUR][1000 genomes]
rs6701988	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72916320	0.86[EUR][1000 genomes]
rs72918447	0.87[EUR][1000 genomes]
rs7512692	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7519639	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7525509	0.91[ASN][1000 genomes]
rs7535076	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7537440	0.92[ASN][1000 genomes]
rs7547794	0.92[ASN][1000 genomes]
rs7547857	0.92[ASN][1000 genomes]
rs7547866	0.92[ASN][1000 genomes]
rs7551301	0.87[EUR][1000 genomes]
rs963140	0.91[ASN][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	nsv1210	chr1:67017295-67033203	Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12565798	SGIP1	cis	Whole Blood	GTEx

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:67000800-67029800	Weak transcription	Primary hematopoietic stem cells	blood
2	chr1:67009800-67028200	Weak transcription	Brain Germinal Matrix	brain
3	chr1:67010000-67029000	Weak transcription	Fetal Kidney	kidney
4	chr1:67011000-67028000	Weak transcription	HUVEC	blood vessel
5	chr1:67011800-67029800	Weak transcription	Fetal Brain Male	brain
6	chr1:67019000-67028600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
7	chr1:67020200-67028200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr1:67022400-67028200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr1:67022400-67028200	Weak transcription	Left Ventricle	heart
10	chr1:67022400-67028200	Weak transcription	NH-A	brain
11	chr1:67022400-67028400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr1:67022400-67028400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr1:67023000-67028400	Weak transcription	NHEK	skin
14	chr1:67023400-67028000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr1:67023400-67028600	Weak transcription	Brain Anterior Caudate	brain
16	chr1:67023400-67028800	Weak transcription	Cortex derived primary cultured neurospheres	brain
17	chr1:67023600-67028200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr1:67023800-67028800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
19	chr1:67024000-67028200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
20	chr1:67025000-67031600	Enhancers	Fetal Lung	lung
21	chr1:67025600-67028000	Weak transcription	Brain Hippocampus Middle	brain
22	chr1:67025600-67028800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr1:67026000-67028800	Weak transcription	Brain Substantia Nigra	brain
24	chr1:67026000-67029000	Weak transcription	Brain Inferior Temporal Lobe	brain
25	chr1:67026200-67028000	Weak transcription	Fetal Heart	heart
26	chr1:67026400-67028200	Enhancers	NHDF-Ad	bronchial
27	chr1:67027200-67028200	Enhancers	NHLF	lung
28	chr1:67027200-67029600	Enhancers	Aorta	Aorta
29	chr1:67027200-67030200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr1:67027200-67032000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr1:67027400-67028800	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr1:67027400-67028800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr1:67027400-67031400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr1:67027600-67028200	Enhancers	Muscle Satellite Cultured Cells	--
35	chr1:67027600-67028800	Enhancers	Hela-S3	cervix
36	chr1:67027600-67028800	Enhancers	Osteobl	bone
37	chr1:67027800-67028200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr1:67027800-67028800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr1:67027800-67029200	Enhancers	Duodenum Smooth Muscle	Duodenum
40	chr1:67027800-67029600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr1:67027800-67029600	Enhancers	Brain Cingulate Gyrus	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links