Variant report

Variant	rs2409007
Chromosome Location	chr5:57529966-57529967
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:57527499..57530106-chr5:57539853..57541635,2	MCF-7	breast:
2	chr5:57528101..57530824-chr5:57745599..57747448,2	MCF-7	breast:
3	chr5:57517523..57520170-chr5:57529878..57532281,2	MCF-7	breast:
4	chr5:57529817..57531823-chr5:57533642..57536408,2	K562	blood:

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs1035473	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10513135	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10513141	0.80[AFR][1000 genomes]
rs11737991	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11738845	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11740290	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11741389	0.80[AFR][1000 genomes]
rs11741711	0.81[AFR][1000 genomes]
rs11742619	1.00[YRI][hapmap]
rs11744441	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11745039	0.80[AFR][1000 genomes]
rs11745219	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11746013	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11746649	0.85[AFR][1000 genomes]
rs11747017	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11749817	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11750320	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11953112	0.86[CHB][hapmap]
rs12515401	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17696079	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17764094	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1971059	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1971060	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4700259	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4700268	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4700269	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4700273	0.82[CEU][hapmap];1.00[CHB][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4700283	0.86[CHB][hapmap]
rs56262220	0.85[AFR][1000 genomes]
rs66884124	0.82[ASN][1000 genomes]
rs72755718	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72755724	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72755726	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72755728	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72755729	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72755745	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72755750	0.95[AFR][1000 genomes];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72755767	0.94[ASN][1000 genomes]
rs72755790	0.80[AFR][1000 genomes]
rs7701350	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs7733184	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs969473	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[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	nsv432746	chr5:57502859-57547419	Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:57521800-57535600	Weak transcription	Skeletal Muscle Female	skeletal muscle
2	chr5:57522600-57531000	Weak transcription	Osteobl	bone
3	chr5:57525200-57535400	Weak transcription	Skeletal Muscle Male	skeletal muscle
4	chr5:57526200-57535600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr5:57526200-57535600	Weak transcription	Psoas Muscle	Psoas
6	chr5:57526200-57544000	Weak transcription	Aorta	Aorta
7	chr5:57526800-57530800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr5:57527200-57530800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr5:57527200-57531000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr5:57527200-57531000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr5:57527200-57531000	Weak transcription	NHEK	skin
12	chr5:57527200-57532600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
13	chr5:57527200-57535600	Weak transcription	HMEC	breast
14	chr5:57527400-57535800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr5:57528200-57530600	Weak transcription	Hela-S3	cervix
16	chr5:57529000-57530600	Enhancers	A549	lung
17	chr5:57529800-57531000	Weak transcription	Breast Myoepithelial Primary Cells	Breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links