Variant report

Variant	rs6883288
Chromosome Location	chr5:154468471-154468472
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:154460850..154462591-chr5:154465930..154468582,2	MCF-7	breast:

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10071858	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10077934	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10078853	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1025301	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12187264	0.84[EUR][1000 genomes]
rs13154769	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13172264	0.94[ASN][1000 genomes]
rs17116820	0.86[ASN][1000 genomes]
rs17116849	0.86[ASN][1000 genomes]
rs17116855	0.86[ASN][1000 genomes]
rs17116862	0.86[ASN][1000 genomes]
rs17116872	0.86[ASN][1000 genomes]
rs17116886	0.86[ASN][1000 genomes]
rs17116912	0.80[ASN][1000 genomes]
rs17116922	0.80[ASN][1000 genomes]
rs17650275	0.87[EUR][1000 genomes]
rs286595	1.00[JPT][hapmap]
rs34974326	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs36059089	0.85[EUR][1000 genomes]
rs6580134	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs66691937	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs66859046	0.88[ASN][1000 genomes]
rs67047831	0.88[ASN][1000 genomes]
rs67562605	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6859744	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6869991	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6870353	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs71597682	0.88[ASN][1000 genomes]
rs7713042	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7715693	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs7719709	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs7722477	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7724975	0.85[EUR][1000 genomes]
rs7733613	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7733811	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7736559	0.84[AMR][1000 genomes];0.89[EUR][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	nsv883059	chr5:154457905-154556230	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:154462200-154474400	Weak transcription	Right Ventricle	heart
2	chr5:154464000-154472000	Enhancers	Placenta	Placenta
3	chr5:154464200-154469200	Weak transcription	HUVEC	blood vessel
4	chr5:154464200-154472800	Enhancers	Placenta Amnion	Placenta Amnion
5	chr5:154464600-154468800	Enhancers	Fetal Stomach	stomach
6	chr5:154465200-154469600	Enhancers	NHEK	skin
7	chr5:154466600-154468800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr5:154466600-154469800	Enhancers	Fetal Heart	heart
9	chr5:154467200-154469200	Enhancers	Ovary	ovary
10	chr5:154467400-154470600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr5:154467400-154470600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr5:154467400-154470600	Weak transcription	HMEC	breast
13	chr5:154467400-154470600	Weak transcription	HSMMtube	muscle
14	chr5:154467400-154474800	Weak transcription	Left Ventricle	heart
15	chr5:154468000-154468600	Enhancers	ES-I3 Cell Line	embryonic stem cell
16	chr5:154468200-154468800	Enhancers	Colon Smooth Muscle	Colon
17	chr5:154468200-154469200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr5:154468200-154470600	Weak transcription	Rectal Smooth Muscle	rectum
19	chr5:154468400-154471400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links