Variant report

Variant	rs17164996
Chromosome Location	chr5:126727739-126727740
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 70 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs10519936	0.85[CEU][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];0.81[JPT][hapmap];0.86[TSI][hapmap];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10519937	0.85[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10519938	0.93[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11743934	0.85[CEU][hapmap]
rs11949373	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11950058	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11950427	0.85[CEU][hapmap];0.86[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11952552	0.85[CEU][hapmap];0.85[EUR][1000 genomes]
rs11952947	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11953024	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11958435	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11959505	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12233927	0.85[CEU][hapmap];0.97[GIH][hapmap];0.82[TSI][hapmap];0.85[EUR][1000 genomes]
rs12234066	0.85[CEU][hapmap];0.85[EUR][1000 genomes]
rs1363385	0.83[CEU][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1363388	0.85[CEU][hapmap];0.97[GIH][hapmap];0.86[TSI][hapmap];0.83[EUR][1000 genomes]
rs1363631	0.85[CEU][hapmap];0.85[EUR][1000 genomes]
rs1422318	0.85[CEU][hapmap];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1529467	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17164902	0.83[EUR][1000 genomes]
rs17164979	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17164995	1.00[CEU][hapmap];0.86[CHB][hapmap];0.92[GIH][hapmap];0.81[JPT][hapmap];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17165090	0.85[CEU][hapmap];0.97[GIH][hapmap];0.82[TSI][hapmap];0.81[EUR][1000 genomes]
rs173509	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17604615	0.88[TSI][hapmap];0.83[EUR][1000 genomes]
rs17604665	0.83[EUR][1000 genomes]
rs17604777	0.84[CEU][hapmap];0.88[EUR][1000 genomes]
rs17604819	0.84[CEU][hapmap];0.86[EUR][1000 genomes]
rs17839693	0.85[CEU][hapmap];0.84[EUR][1000 genomes]
rs17839695	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2068168	0.84[CEU][hapmap];0.88[EUR][1000 genomes]
rs2408871	0.85[CEU][hapmap];0.86[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2898044	0.84[EUR][1000 genomes]
rs3756721	0.85[CEU][hapmap];0.97[GIH][hapmap]
rs3812054	0.84[CEU][hapmap];0.88[TSI][hapmap];0.87[EUR][1000 genomes]
rs3812055	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[TSI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3844184	0.85[CEU][hapmap];0.94[GIH][hapmap]
rs3851469	0.85[CEU][hapmap];0.97[GIH][hapmap]
rs3909351	0.85[CEU][hapmap]
rs4563674	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56006993	0.84[EUR][1000 genomes]
rs59745967	0.81[EUR][1000 genomes]
rs60153933	0.81[EUR][1000 genomes]
rs6595764	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6595765	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6595767	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[TSI][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6595768	0.84[CEU][hapmap];0.88[TSI][hapmap];0.87[EUR][1000 genomes]
rs6595769	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[TSI][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67200948	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67854568	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs68035691	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6874392	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6874521	1.00[CEU][hapmap];0.86[CHB][hapmap];0.81[JPT][hapmap];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6874752	0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6881894	0.85[CEU][hapmap];0.97[GIH][hapmap];0.86[TSI][hapmap];0.83[EUR][1000 genomes]
rs6888010	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6891785	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6892742	0.81[EUR][1000 genomes]
rs6897290	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72788578	0.83[EUR][1000 genomes]
rs72788581	0.83[EUR][1000 genomes]
rs72788599	0.87[EUR][1000 genomes]
rs72790422	0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72790424	0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72790426	0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]

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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17164996	SLC12A2	cis	cerebellum	SCAN

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:126691000-126746000	Weak transcription	Fetal Muscle Trunk	muscle
2	chr5:126707800-126729000	Weak transcription	Brain Substantia Nigra	brain
3	chr5:126707800-126731600	Weak transcription	Brain Anterior Caudate	brain
4	chr5:126710000-126731800	Weak transcription	H1 Cell Line	embryonic stem cell
5	chr5:126710200-126741200	Weak transcription	HUES64 Cell Line	embryonic stem cell
6	chr5:126712800-126734200	Weak transcription	HUES48 Cell Line	embryonic stem cell
7	chr5:126714800-126732200	Weak transcription	HSMMtube	muscle
8	chr5:126715200-126731600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr5:126720000-126732400	Weak transcription	Brain Cingulate Gyrus	brain
10	chr5:126720000-126732400	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr5:126720000-126742000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr5:126720600-126728000	Weak transcription	Cortex derived primary cultured neurospheres	brain
13	chr5:126720800-126729000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr5:126722800-126736000	Weak transcription	HSMM	muscle
15	chr5:126723000-126728400	Weak transcription	Muscle Satellite Cultured Cells	--
16	chr5:126725000-126731800	Weak transcription	Fetal Muscle Leg	muscle
17	chr5:126725400-126728000	Weak transcription	Brain Hippocampus Middle	brain
18	chr5:126726200-126728800	Weak transcription	Brain Angular Gyrus	brain

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