Variant report

Variant	rs17111445
Chromosome Location	chr12:72964753-72964754
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 61 )
Associated
traits (count: 22 )

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

rs_ID	r²[population]
rs10161472	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs10784980	1.00[EUR][1000 genomes]
rs10879422	1.00[CEU][hapmap]
rs10879432	1.00[CEU][hapmap]
rs10879433	1.00[CEU][hapmap]
rs10879435	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10879438	1.00[CEU][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10879440	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10879441	1.00[CEU][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10879467	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs10879468	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs10879469	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs10879470	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs10879471	1.00[EUR][1000 genomes]
rs11179236	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11179241	1.00[YRI][hapmap]
rs11179242	1.00[CEU][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11179251	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11179252	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11179265	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11179278	0.96[EUR][1000 genomes]
rs11179283	1.00[EUR][1000 genomes]
rs11179285	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs11179291	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs11179301	1.00[EUR][1000 genomes]
rs11179306	1.00[EUR][1000 genomes]
rs12297047	1.00[CEU][hapmap]
rs12301567	1.00[CEU][hapmap]
rs12322905	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12367387	1.00[CEU][hapmap]
rs12370001	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs12370471	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs12372580	0.84[AMR][1000 genomes]
rs1387977	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs1444602	1.00[CEU][hapmap]
rs17111240	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs17111392	1.00[CEU][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17111405	1.00[CEU][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17111496	1.00[CEU][hapmap];0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1821310	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs1821311	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs2217678	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs7139238	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs7308664	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs74105937	0.98[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 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	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
4	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
5	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
6	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
7	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
8	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
9	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
10	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
11	nsv832454	chr12:72940798-73081180	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
12	esv1805187	chr12:72949787-73013475	Enhancers Strong transcription Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
13	nsv559365	chr12:72955245-72966727	Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region	1 gene(s)	inside rSNPs	diseases
14	nsv559366	chr12:72956100-72968492	Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats	TF binding region	1 gene(s)	inside rSNPs	diseases
15	esv1826697	chr12:72962655-72968492	Weak transcription Enhancers	n/a	n/a	inside rSNPs	diseases
16	esv1848753	chr12:72962655-72968492	Enhancers Weak transcription	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:22)

SNP	Gene	Cis/trans	Tissue	Source
rs17111445	RPL6	cis	Temporal Cortex	GTEx
rs17111445	TMSL3	cis	Temporal Cortex	GTEx
rs17111445	TM9SF4	cis	Temporal Cortex	GTEx
rs17111445	FCHSD2	cis	Temporal Cortex	GTEx
rs17111445	RPS6KA1	cis	Temporal Cortex	GTEx
rs17111445	SIPA1	cis	Temporal Cortex	GTEx
rs17111445	HERC5	cis	Temporal Cortex	GTEx
rs17111445	SFRS14	cis	Temporal Cortex	GTEx
rs17111445	ZNF280B	cis	Temporal Cortex	GTEx
rs17111445	ATP5I	cis	Temporal Cortex	GTEx
rs17111445	RPS29	cis	Temporal Cortex	GTEx
rs17111445	DUSP23	cis	Temporal Cortex	GTEx
rs17111445	PPFIA2	cis	Temporal Cortex	GTEx
rs17111445	NEFL	cis	Temporal Cortex	GTEx
rs17111445	ANKRD57	cis	Temporal Cortex	GTEx
rs17111445	CNTNAP1	cis	Temporal Cortex	GTEx
rs17111445	GAP43	cis	Temporal Cortex	GTEx
rs17111445	RPS8	cis	Temporal Cortex	GTEx
rs17111445	LPHN1	cis	Temporal Cortex	GTEx
rs17111445	GIMAP8	cis	Temporal Cortex	GTEx
rs17111445	C12orf75	cis	Temporal Cortex	GTEx
rs17111445	SERBP1	cis	Temporal Cortex	GTEx

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:72947600-72973600	Weak transcription	Fetal Intestine Small	intestine
2	chr12:72956400-72973800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr12:72958200-72984400	Weak transcription	Pancreas	Pancrea
4	chr12:72964400-72986800	Weak transcription	Fetal Intestine Large	intestine
5	chr12:72964600-72965200	Enhancers	iPS-18 Cell Line	embryonic stem cell

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