Variant report

Variant	rs1660579
Chromosome Location	chr11:76537114-76537115
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:76497234..76499501-chr11:76534793..76537709,2	K562	blood:
2	chr11:76350867..76353038-chr11:76535438..76537747,2	MCF-7	breast:
3	chr11:76536619..76538688-chr11:76571943..76573474,2	K562	blood:

Variant related genes	Relation type
ENSG00000078124	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10736812	0.87[GIH][hapmap]
rs10793223	0.81[GIH][hapmap]
rs10793227	0.87[GIH][hapmap]
rs10793231	0.87[GIH][hapmap]
rs10899341	0.87[GIH][hapmap]
rs10899344	0.88[GIH][hapmap]
rs1149577	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1149626	0.87[CEU][hapmap];0.91[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1224951	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1224952	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1225127	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1225129	0.83[EUR][1000 genomes]
rs1225131	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs1225132	1.00[CEU][hapmap];0.94[TSI][hapmap];0.83[EUR][1000 genomes]
rs1225133	0.80[EUR][1000 genomes]
rs1225134	0.83[EUR][1000 genomes]
rs1225135	0.83[EUR][1000 genomes]
rs1225136	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs1225137	0.83[EUR][1000 genomes]
rs1225139	1.00[CEU][hapmap];0.88[GIH][hapmap];0.82[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1225140	1.00[CEU][hapmap];0.94[TSI][hapmap];0.83[EUR][1000 genomes]
rs1225141	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs1225147	0.83[EUR][1000 genomes]
rs1225149	0.81[EUR][1000 genomes]
rs1234832	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1235157	1.00[CEU][hapmap];0.94[TSI][hapmap];0.83[EUR][1000 genomes]
rs12794575	0.80[CEU][hapmap]
rs1372045	0.88[CEU][hapmap];0.84[TSI][hapmap]
rs1372046	0.87[CEU][hapmap]
rs1517907	0.81[CEU][hapmap]
rs1589126	0.87[GIH][hapmap]
rs2451908	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2826	0.87[GIH][hapmap]
rs3740765	0.87[GIH][hapmap]
rs3740767	0.84[GIH][hapmap]
rs3824889	0.84[GIH][hapmap]
rs4457775	0.81[CEU][hapmap]
rs4944132	0.80[CEU][hapmap]
rs4944134	0.87[GIH][hapmap]
rs4945129	0.84[GIH][hapmap]
rs591043	0.87[CEU][hapmap];0.87[GIH][hapmap]
rs6592671	0.88[CEU][hapmap]
rs6592683	0.84[GIH][hapmap]
rs7110532	0.84[GIH][hapmap]
rs7113290	0.81[CEU][hapmap]
rs7123496	0.87[GIH][hapmap]
rs7924613	0.86[CEU][hapmap];0.81[GIH][hapmap]
rs7925135	0.81[CEU][hapmap];0.84[GIH][hapmap]
rs7925774	0.87[GIH][hapmap]
rs7927367	0.85[CEU][hapmap]
rs7931561	0.81[CEU][hapmap]
rs7932288	0.81[CEU][hapmap]
rs7943913	0.84[GIH][hapmap]

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	nsv897931	chr11:76489673-76540708	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs1660579	ODZ4	cis	parietal	SCAN
rs1660579	ACER3	cis	parietal	SCAN
rs1660579	NEU3	cis	parietal	SCAN
rs1660579	LIPT2	cis	parietal	SCAN
rs1660579	CAPN5	cis	parietal	SCAN
rs1660579	GDPD5	cis	parietal	SCAN
rs1660579	ACER3	cis	lymphoblastoid	seeQTL
rs1660579	ACER3	cis	cerebellum	SCAN

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:76533600-76537400	Enhancers	Breast Myoepithelial Primary Cells	Breast
2	chr11:76533600-76537400	Enhancers	HMEC	breast
3	chr11:76534200-76537400	Enhancers	Primary monocytes fromperipheralblood	blood
4	chr11:76534400-76537200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
5	chr11:76534400-76537200	Enhancers	Placenta	Placenta
6	chr11:76534400-76537400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr11:76534600-76537200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr11:76534600-76537200	Enhancers	Primary hematopoietic stem cells short term culture	blood
9	chr11:76534600-76537200	Enhancers	Spleen	Spleen
10	chr11:76534800-76537400	Enhancers	Adipose Nuclei	Adipose
11	chr11:76535200-76541400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr11:76535400-76546400	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr11:76535400-76549000	Weak transcription	Small Intestine	intestine
14	chr11:76535600-76537200	Enhancers	HUVEC	blood vessel
15	chr11:76535800-76537400	Enhancers	Hela-S3	cervix
16	chr11:76535800-76537400	Enhancers	Monocytes-CD14+_RO01746	blood
17	chr11:76536200-76537400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr11:76536400-76537200	Flanking Active TSS	K562	blood
19	chr11:76536400-76537400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr11:76536400-76544600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr11:76536600-76537200	Enhancers	Primary hematopoietic stem cells	blood
22	chr11:76536600-76537200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr11:76536800-76537400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr11:76536800-76537400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr11:76536800-76537400	Enhancers	NHEK	skin
26	chr11:76536800-76540600	Weak transcription	Lung	lung
27	chr11:76536800-76547800	Weak transcription	Left Ventricle	heart

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links