Variant report

Variant	rs7709401
Chromosome Location	chr5:54062928-54062929
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:53813350..53815474-chr5:54061824..54064648,2	MCF-7	breast:
2	chr5:54058549..54060576-chr5:54060806..54063597,3	K562	blood:
3	chr5:54036001..54038527-chr5:54062839..54065440,2	MCF-7	breast:
4	chr5:54040322..54042008-chr5:54061113..54064039,2	K562	blood:
5	chr5:54061560..54063270-chr5:54063643..54065154,2	K562	blood:

Variant related genes	Relation type
ENSG00000178996	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10039924	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10042288	0.82[EUR][1000 genomes]
rs10042495	0.82[EUR][1000 genomes]
rs10045790	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10050561	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10053168	0.82[ASN][1000 genomes]
rs10058862	0.81[EUR][1000 genomes]
rs10061958	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10066294	0.88[EUR][1000 genomes]
rs10068073	0.92[ASN][1000 genomes]
rs10071183	0.90[ASN][1000 genomes]
rs10073662	0.90[ASN][1000 genomes]
rs10073721	0.90[ASN][1000 genomes]
rs10073837	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs10434559	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10461588	0.82[ASN][1000 genomes]
rs10805463	0.82[ASN][1000 genomes]
rs10940427	0.88[EUR][1000 genomes]
rs11950757	0.93[ASN][1000 genomes]
rs11959080	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13186826	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs16883428	0.89[ASN][1000 genomes]
rs1867685	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs4242044	0.90[ASN][1000 genomes]
rs4282277	0.92[ASN][1000 genomes]
rs4290968	0.82[ASN][1000 genomes]
rs4292417	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4298212	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4336310	0.82[ASN][1000 genomes]
rs4356994	0.90[ASN][1000 genomes]
rs4457032	0.82[ASN][1000 genomes]
rs4498213	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4515247	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4527555	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4865870	0.84[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs4865872	0.90[ASN][1000 genomes]
rs4865873	0.82[ASN][1000 genomes]
rs4865874	0.82[ASN][1000 genomes]
rs59595173	0.97[ASN][1000 genomes]
rs59664922	0.97[ASN][1000 genomes]
rs60548640	1.00[ASN][1000 genomes]
rs6450247	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6450248	0.97[ASN][1000 genomes]
rs6860729	0.92[ASN][1000 genomes]
rs6863705	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6867867	0.90[ASN][1000 genomes]
rs6892315	0.90[ASN][1000 genomes]
rs6899052	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs73126822	0.97[ASN][1000 genomes]
rs73126828	0.97[ASN][1000 genomes]
rs73126830	0.97[ASN][1000 genomes]
rs7709225	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7726707	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9292072	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9292073	0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv880717	chr5:54025701-54106378	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
2	nsv830300	chr5:54056300-54257344	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:54060600-54070000	Weak transcription	Fetal Muscle Leg	muscle
2	chr5:54061000-54070400	Weak transcription	NHLF	lung
3	chr5:54061200-54067000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr5:54062000-54063600	Weak transcription	Primary B cells from peripheral blood	blood
5	chr5:54062000-54064000	Weak transcription	HSMMtube	muscle
6	chr5:54062600-54063000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links