Variant report

Variant	rs12325234
Chromosome Location	chr16:71459628-71459629
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr16:71452691..71455669-chr16:71459394..71461176,2	MCF-7	breast:
2	chr16:71457633..71459826-chr16:71493522..71496195,3	K562	blood:
3	chr16:71451545..71453990-chr16:71457536..71460317,2	K562	blood:

Variant related genes	Relation type
ENSG00000247324	Chromatin interaction
ENSG00000167377	Chromatin interaction
ENSG00000262120	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10468265	0.90[CEU][hapmap]
rs12149254	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12444212	0.82[EUR][1000 genomes]
rs12444714	1.00[CEU][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12448992	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12918320	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12919092	1.00[CEU][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12922597	0.87[EUR][1000 genomes]
rs12922830	0.86[EUR][1000 genomes]
rs16972808	0.90[CEU][hapmap]
rs16973112	0.90[CEU][hapmap]
rs16973190	0.90[CEU][hapmap]
rs17343777	0.82[EUR][1000 genomes]
rs2033251	1.00[YRI][hapmap];0.96[AFR][1000 genomes]
rs2052873	0.90[CEU][hapmap]
rs34400718	0.92[EUR][1000 genomes]
rs35166226	0.82[EUR][1000 genomes]
rs3886947	0.89[CEU][hapmap]
rs6499520	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs66778248	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs8051439	0.89[CEU][hapmap]
rs8056735	0.90[CEU][hapmap]

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	nsv949461	chr16:71196153-71579711	ZNF genes & repeats Enhancers Weak transcription Genic enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
2	nsv1064435	chr16:71440719-71488771	Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Enhancers Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12325234	ZNF23	cis	brain	BrainEAC
rs12325234	RP11-510M2.10	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:71457000-71461000	Weak transcription	Right Atrium	heart
2	chr16:71459200-71459800	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
3	chr16:71459200-71460000	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
4	chr16:71459200-71461200	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
5	chr16:71459400-71459800	Flanking Active TSS	HepG2	liver
6	chr16:71459400-71460000	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
7	chr16:71459400-71460800	Active TSS	H1 Cell Line	embryonic stem cell
8	chr16:71459400-71460800	Active TSS	H9 Cell Line	embryonic stem cell
9	chr16:71459400-71460800	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
10	chr16:71459400-71461000	Active TSS	iPS-15b Cell Line	embryonic stem cell
11	chr16:71459600-71459800	Flanking Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr16:71459600-71459800	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr16:71459600-71459800	Flanking Bivalent TSS/Enh	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr16:71459600-71459800	Bivalent/Poised TSS	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr16:71459600-71459800	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr16:71459600-71459800	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr16:71459600-71459800	Bivalent/Poised TSS	NHEK	skin
18	chr16:71459600-71460000	Flanking Bivalent TSS/Enh	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr16:71459600-71460000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr16:71459600-71460000	Flanking Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr16:71459600-71460000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr16:71459600-71460200	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr16:71459600-71460400	Active TSS	HUES48 Cell Line	embryonic stem cell
24	chr16:71459600-71460400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr16:71459600-71460400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
26	chr16:71459600-71460400	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr16:71459600-71460400	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr16:71459600-71460400	ZNF genes & repeats	Spleen	Spleen
29	chr16:71459600-71460400	Flanking Active TSS	HMEC	breast
30	chr16:71459600-71460800	Active TSS	A549	lung
31	chr16:71459600-71461000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr16:71459600-71461000	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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