Variant report

Variant	rs2409006
Chromosome Location	chr5:57530030-57530031
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: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs1562242	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1862540	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1972647	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2910578	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2910579	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2910581	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2910582	0.80[AFR][1000 genomes]
rs2910583	0.80[AFR][1000 genomes]
rs2910586	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2910606	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2962007	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2962025	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2964190	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2964192	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2964194	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2964196	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2964197	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2964198	0.82[EUR][1000 genomes]
rs2964201	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs37489	0.83[AMR][1000 genomes]
rs37491	0.83[AMR][1000 genomes]
rs37513	0.84[AMR][1000 genomes]
rs37514	0.84[AMR][1000 genomes]
rs37515	0.85[AMR][1000 genomes]
rs37517	0.85[AMR][1000 genomes]
rs37518	0.85[AMR][1000 genomes]
rs37525	0.82[AMR][1000 genomes]
rs37529	0.82[AMR][1000 genomes]
rs37530	0.82[AMR][1000 genomes]
rs40531	0.85[AMR][1000 genomes]
rs7715909	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs972060	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs972061	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[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