Variant report

Variant	rs13215054
Chromosome Location	chr6:28502794-28502795
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:28499347..28503956-chr6:28505758..28508912,7	K562	blood:
2	chr6:28498885..28501651-chr6:28502273..28504670,3	K562	blood:
3	chr6:28455084..28458229-chr6:28499553..28502958,3	K562	blood:

Extended variants
information (count: 27 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs1005126	0.92[CHB][hapmap]
rs11751928	0.92[CHB][hapmap]
rs11755387	0.83[CHB][hapmap]
rs13190937	0.92[CHB][hapmap]
rs13196606	0.92[CHB][hapmap]
rs13199081	0.92[CHB][hapmap]
rs13215804	0.92[CHB][hapmap];0.96[CHD][hapmap]
rs13217047	0.88[AFR][1000 genomes]
rs16894011	0.83[CHB][hapmap]
rs17336532	0.80[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs17856167	0.83[CHB][hapmap]
rs2232427	0.83[CHB][hapmap]
rs2394102	0.81[ASN][1000 genomes]
rs3799499	0.82[CHB][hapmap]
rs3799500	0.92[CHB][hapmap]
rs41270599	0.83[AFR][1000 genomes]
rs6902687	0.91[CHB][hapmap]
rs6905380	0.92[CHB][hapmap]
rs7754960	0.92[CHB][hapmap]
rs7774981	0.92[CHB][hapmap]
rs9468358	0.92[CHB][hapmap]
rs9468364	0.82[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv462666	chr6:28417222-28574415	Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS Flanking Bivalent TSS/Enh Enhancers Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
2	nsv601210	chr6:28417222-28574415	Active TSS Bivalent/Poised TSS Weak transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
3	nsv1020689	chr6:28449137-28635171	Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
4	nsv830621	chr6:28473951-28675709	Bivalent/Poised TSS Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
5	nsv601211	chr6:28483482-28521316	Bivalent Enhancer Active TSS Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs13215054	LRRC16A	cis	parietal	SCAN
rs13215054	ZNF323	cis	parietal	SCAN
rs13215054	ZNF192	cis	cerebellum	SCAN
rs13215054	ZFP57	cis	multi-tissue	Pritchard
rs13215054	ZSCAN12	Cis_1M	lymphoblastoid	RTeQTL
rs13215054	ZSCAN23	cis	parietal	SCAN
rs13215054	BTN3A2	Cis_chr	lymphoblastoid	RTeQTL
rs13215054	HLA-H	cis	multi-tissue	Pritchard
rs13215054	HLA-A	cis	multi-tissue	Pritchard
rs13215054	BTN3A2///BTN3A3	Cis_chr	lymphoblastoid	RTeQTL
rs13215054	BTN3A2	cis	multi-tissue	Pritchard
rs13215054	ZSCAN23	cis	cerebellum	SCAN
rs13215054	ZFP57	Cis_chr	lymphoblastoid	RTeQTL

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28500000-28504400	Weak transcription	HUES64 Cell Line	embryonic stem cell
2	chr6:28500000-28504600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr6:28502200-28504400	Enhancers	K562	blood

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