Variant report

Variant	rs17164935
Chromosome Location	chr5:126791282-126791283
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 79 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs10519936	0.85[CEU][hapmap];0.89[TSI][hapmap];0.83[EUR][1000 genomes]
rs10519937	0.85[CEU][hapmap]
rs10519938	0.85[CEU][hapmap]
rs11743934	0.85[CEU][hapmap];0.81[JPT][hapmap];0.85[YRI][hapmap];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11949330	0.83[EUR][1000 genomes]
rs11950427	0.85[CEU][hapmap]
rs11952366	0.83[EUR][1000 genomes]
rs11952552	0.85[CEU][hapmap];0.85[EUR][1000 genomes]
rs11959505	0.85[CEU][hapmap]
rs12233927	0.85[CEU][hapmap];0.93[TSI][hapmap];0.85[EUR][1000 genomes]
rs12234066	0.85[CEU][hapmap];0.85[EUR][1000 genomes]
rs1363385	0.83[CEU][hapmap]
rs1363388	0.85[CEU][hapmap];0.89[TSI][hapmap];0.81[EUR][1000 genomes]
rs1363631	0.85[CEU][hapmap];0.85[EUR][1000 genomes]
rs1422318	0.85[CEU][hapmap];0.83[EUR][1000 genomes]
rs1593949	0.83[EUR][1000 genomes]
rs1593950	0.83[EUR][1000 genomes]
rs17164903	0.86[EUR][1000 genomes]
rs17164915	0.83[EUR][1000 genomes]
rs17164995	0.81[EUR][1000 genomes]
rs17165090	0.85[CEU][hapmap];0.93[TSI][hapmap];0.86[EUR][1000 genomes]
rs17444885	1.00[CEU][hapmap]
rs17604615	1.00[CEU][hapmap];0.96[GIH][hapmap];0.85[TSI][hapmap];0.81[EUR][1000 genomes]
rs17604665	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs17604777	0.84[CEU][hapmap];0.80[EUR][1000 genomes]
rs17604819	0.84[CEU][hapmap];0.81[EUR][1000 genomes]
rs17604882	1.00[CEU][hapmap]
rs17604889	1.00[CEU][hapmap];0.96[GIH][hapmap]
rs17604946	1.00[CEU][hapmap]
rs17673474	1.00[CEU][hapmap]
rs17673517	1.00[CEU][hapmap]
rs17673685	1.00[CEU][hapmap];0.96[GIH][hapmap];0.81[EUR][1000 genomes]
rs17839693	0.85[CEU][hapmap];0.83[EUR][1000 genomes]
rs2068168	0.84[CEU][hapmap];0.80[EUR][1000 genomes]
rs2173978	0.83[EUR][1000 genomes]
rs2408871	0.85[CEU][hapmap]
rs2408873	0.82[EUR][1000 genomes]
rs2434620	0.84[EUR][1000 genomes]
rs3756721	0.85[CEU][hapmap];0.81[JPT][hapmap];0.89[TSI][hapmap];0.84[EUR][1000 genomes]
rs3812053	0.81[EUR][1000 genomes]
rs3812054	0.84[CEU][hapmap];0.96[GIH][hapmap];0.85[TSI][hapmap];0.81[EUR][1000 genomes]
rs3844184	0.85[CEU][hapmap];0.89[TSI][hapmap];0.85[EUR][1000 genomes]
rs3851469	0.85[CEU][hapmap];0.89[TSI][hapmap];0.85[EUR][1000 genomes]
rs3909351	0.85[CEU][hapmap]
rs41298308	0.81[EUR][1000 genomes]
rs41298312	0.81[EUR][1000 genomes]
rs4395678	0.81[EUR][1000 genomes]
rs4604231	0.86[EUR][1000 genomes]
rs55663031	0.86[EUR][1000 genomes]
rs55763657	0.86[EUR][1000 genomes]
rs56006993	0.84[EUR][1000 genomes]
rs57411417	0.86[EUR][1000 genomes]
rs59745967	0.86[EUR][1000 genomes]
rs60153933	0.85[EUR][1000 genomes]
rs60901740	0.86[EUR][1000 genomes]
rs61175766	0.84[EUR][1000 genomes]
rs6595768	0.84[CEU][hapmap];0.96[GIH][hapmap];0.85[TSI][hapmap];0.81[EUR][1000 genomes]
rs67425941	0.86[EUR][1000 genomes]
rs6874521	0.81[EUR][1000 genomes]
rs6881894	0.85[CEU][hapmap];0.89[TSI][hapmap];0.81[EUR][1000 genomes]
rs72788578	0.81[EUR][1000 genomes]
rs72788581	0.81[EUR][1000 genomes]
rs72788599	0.81[EUR][1000 genomes]
rs72790418	0.81[EUR][1000 genomes]
rs72790419	0.81[EUR][1000 genomes]
rs72790428	0.81[EUR][1000 genomes]
rs72790430	0.81[EUR][1000 genomes]
rs72790433	0.81[EUR][1000 genomes]
rs72790438	0.81[EUR][1000 genomes]
rs72790443	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72790444	0.81[EUR][1000 genomes]
rs72790451	0.81[EUR][1000 genomes]
rs7700469	0.83[EUR][1000 genomes]
rs7737871	0.82[YRI][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	nsv1033607	chr5:126385181-127304459	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	nsv1019821	chr5:126658200-126934917	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv537894	chr5:126658200-126934917	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv1032587	chr5:126691103-126826978	Genic enhancers Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv830478	chr5:126721368-126937408	Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs17164935	SLC12A2	cis	cerebellum	SCAN
rs17164935	PRRC1	cis	cerebellum	SCAN

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:126742800-126792400	Weak transcription	HUES64 Cell Line	embryonic stem cell
2	chr5:126763400-126794000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr5:126774600-126798800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
4	chr5:126778000-126795400	Weak transcription	Brain Angular Gyrus	brain
5	chr5:126781800-126794800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr5:126782600-126795200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr5:126783200-126794000	Strong transcription	HUES48 Cell Line	embryonic stem cell
8	chr5:126783400-126795600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr5:126783800-126797200	Weak transcription	HSMM	muscle
10	chr5:126784400-126791400	Strong transcription	HSMMtube	muscle
11	chr5:126785200-126797000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
12	chr5:126785400-126794800	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr5:126786000-126797600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr5:126787400-126791400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr5:126787400-126793400	Strong transcription	Cortex derived primary cultured neurospheres	brain
16	chr5:126788200-126792400	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr5:126788800-126792400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr5:126788800-126797800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr5:126789400-126791400	Strong transcription	Brain Anterior Caudate	brain
20	chr5:126789400-126797000	Weak transcription	Brain Substantia Nigra	brain
21	chr5:126789800-126797000	Weak transcription	Brain Cingulate Gyrus	brain
22	chr5:126789800-126830400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
23	chr5:126790200-126793400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
24	chr5:126790200-126797200	Weak transcription	Brain Hippocampus Middle	brain
25	chr5:126790400-126793000	Weak transcription	H1 Cell Line	embryonic stem cell
26	chr5:126790800-126792400	Weak transcription	Fetal Muscle Leg	muscle
27	chr5:126791200-126791600	Strong transcription	Fetal Muscle Trunk	muscle

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