Variant report

Variant	rs10879438
Chromosome Location	chr12:72925229-72925230
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 56 )
Associated
traits (count: 22 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10161472	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs10784980	0.90[EUR][1000 genomes]
rs10879422	1.00[CEU][hapmap]
rs10879432	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs10879433	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs10879435	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10879440	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10879441	1.00[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10879467	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs10879468	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs10879469	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs10879470	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs10879471	0.90[EUR][1000 genomes]
rs11179236	1.00[CEU][hapmap];0.83[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11179241	1.00[YRI][hapmap]
rs11179242	1.00[CEU][hapmap];0.85[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11179251	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11179252	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11179265	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11179278	0.86[EUR][1000 genomes]
rs11179283	0.90[EUR][1000 genomes]
rs11179285	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs11179291	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs11179301	0.90[EUR][1000 genomes]
rs11179306	0.90[EUR][1000 genomes]
rs12297047	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs12301567	1.00[CEU][hapmap]
rs12322905	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12367387	1.00[CEU][hapmap]
rs12370001	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs12370471	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs12372580	0.84[AMR][1000 genomes]
rs1387977	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs1444602	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs17111240	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs17111392	1.00[CEU][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17111405	1.00[CEU][hapmap];0.85[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17111445	1.00[CEU][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17111496	1.00[CEU][hapmap];0.85[YRI][hapmap];0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1821310	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs1821311	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs2217678	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs7139238	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs7308664	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs74105937	0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2422452	chr12:72485933-73175581	Flanking Bivalent TSS/Enh Active TSS Weak transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer 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	19 gene(s)	inside rSNPs	diseases
2	nsv899257	chr12:72569746-73145896	ZNF genes & repeats Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
3	nsv899258	chr12:72624088-72957899	Bivalent Enhancer Weak transcription Bivalent/Poised TSS Flanking Active TSS Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	nsv1044083	chr12:72647640-73275526	Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Genic enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
5	nsv469465	chr12:72655925-73259114	Weak transcription Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
6	nsv559363	chr12:72655925-73259114	Weak transcription Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
7	nsv868884	chr12:72664763-73241518	Enhancers Bivalent/Poised TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
8	nsv832453	chr12:72778058-72966827	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
9	nsv817280	chr12:72820558-73508605	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
10	nsv899259	chr12:72885554-73011367	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
11	nsv899260	chr12:72914831-72977526	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:22)

SNP	Gene	Cis/trans	Tissue	Source
rs10879438	SIPA1	cis	Temporal Cortex	GTEx
rs10879438	LPHN1	cis	Temporal Cortex	GTEx
rs10879438	PPFIA2	cis	Temporal Cortex	GTEx
rs10879438	SERBP1	cis	Temporal Cortex	GTEx
rs10879438	GIMAP8	cis	Temporal Cortex	GTEx
rs10879438	TMSL3	cis	Temporal Cortex	GTEx
rs10879438	NEFL	cis	Temporal Cortex	GTEx
rs10879438	GAP43	cis	Temporal Cortex	GTEx
rs10879438	FCHSD2	cis	Temporal Cortex	GTEx
rs10879438	RPS8	cis	Temporal Cortex	GTEx
rs10879438	TM9SF4	cis	Temporal Cortex	GTEx
rs10879438	RPS6KA1	cis	Temporal Cortex	GTEx
rs10879438	RPL6	cis	Temporal Cortex	GTEx
rs10879438	ATP5I	cis	Temporal Cortex	GTEx
rs10879438	CNTNAP1	cis	Temporal Cortex	GTEx
rs10879438	DUSP23	cis	Temporal Cortex	GTEx
rs10879438	RPS29	cis	Temporal Cortex	GTEx
rs10879438	ZNF280B	cis	Temporal Cortex	GTEx
rs10879438	ANKRD57	cis	Temporal Cortex	GTEx
rs10879438	C12orf75	cis	Temporal Cortex	GTEx
rs10879438	SFRS14	cis	Temporal Cortex	GTEx
rs10879438	HERC5	cis	Temporal Cortex	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:72924200-72925600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr12:72924800-72929000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr12:72924800-72929800	Weak transcription	HUES64 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links