Variant report

Variant	rs11950427
Chromosome Location	chr5:126769146-126769147
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 110 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:105)

rs_ID	r²[population]
rs10519936	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.88[MEX][hapmap];0.93[ASN][1000 genomes]
rs10519937	1.00[CEU][hapmap];0.89[JPT][hapmap];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10519938	1.00[CEU][hapmap];0.86[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];0.81[TSI][hapmap];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11743934	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs11949330	0.81[EUR][1000 genomes]
rs11949373	0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11950058	0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11952366	0.82[EUR][1000 genomes]
rs11952552	1.00[CEU][hapmap];0.82[YRI][hapmap]
rs11952947	0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11953024	0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11956397	0.81[YRI][hapmap]
rs11958435	0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11959505	1.00[CEU][hapmap];0.86[CHB][hapmap];0.89[JPT][hapmap];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12233927	1.00[CEU][hapmap];0.97[GIH][hapmap];0.88[MEX][hapmap];0.82[YRI][hapmap]
rs12234066	1.00[CEU][hapmap];0.87[YRI][hapmap]
rs1363385	0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1363388	1.00[CEU][hapmap];0.83[CHD][hapmap];0.97[GIH][hapmap]
rs1363631	1.00[CEU][hapmap];0.82[YRI][hapmap]
rs1422318	1.00[CEU][hapmap];0.86[CHB][hapmap];0.91[ASN][1000 genomes]
rs1529467	0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1593949	0.82[EUR][1000 genomes]
rs1593950	0.82[EUR][1000 genomes]
rs17164902	0.87[EUR][1000 genomes]
rs17164915	0.82[EUR][1000 genomes]
rs17164935	0.85[CEU][hapmap]
rs17164951	0.95[YRI][hapmap]
rs17164956	0.81[YRI][hapmap]
rs17164957	0.90[YRI][hapmap]
rs17164963	0.81[YRI][hapmap]
rs17164979	0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17164995	0.85[CEU][hapmap];1.00[CHB][hapmap];0.92[GIH][hapmap];0.93[ASN][1000 genomes]
rs17164996	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]
rs17165090	1.00[CEU][hapmap];0.97[GIH][hapmap];0.88[MEX][hapmap];0.82[YRI][hapmap]
rs173509	0.96[ASN][1000 genomes]
rs17444885	0.85[CEU][hapmap];0.83[EUR][1000 genomes]
rs17604615	0.85[CEU][hapmap]
rs17604665	0.85[CEU][hapmap]
rs17604882	0.85[CEU][hapmap];0.83[EUR][1000 genomes]
rs17604889	0.85[CEU][hapmap];0.88[TSI][hapmap];0.83[EUR][1000 genomes]
rs17604946	0.85[CEU][hapmap];0.83[EUR][1000 genomes]
rs17673474	0.85[CEU][hapmap];0.83[EUR][1000 genomes]
rs17673517	0.85[CEU][hapmap];0.83[EUR][1000 genomes]
rs17673685	0.85[CEU][hapmap];0.88[TSI][hapmap];0.84[EUR][1000 genomes]
rs17839690	0.94[EUR][1000 genomes]
rs17839693	1.00[CEU][hapmap];0.87[YRI][hapmap]
rs17839695	0.85[CEU][hapmap];0.86[CHB][hapmap];0.89[JPT][hapmap];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2173978	0.82[EUR][1000 genomes]
rs2408871	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2898044	0.84[EUR][1000 genomes]
rs3756721	1.00[CEU][hapmap];0.97[GIH][hapmap];0.86[MEX][hapmap];0.82[EUR][1000 genomes]
rs3812053	0.84[EUR][1000 genomes]
rs3812055	0.85[CEU][hapmap];0.86[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];0.80[TSI][hapmap];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3844184	1.00[CEU][hapmap];0.94[GIH][hapmap];0.88[MEX][hapmap]
rs3851469	1.00[CEU][hapmap];0.97[GIH][hapmap];0.88[MEX][hapmap];0.90[YRI][hapmap]
rs3909351	1.00[CEU][hapmap]
rs41298308	0.84[EUR][1000 genomes]
rs41298312	0.84[EUR][1000 genomes]
rs4395678	0.83[EUR][1000 genomes]
rs4563674	0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4637594	0.85[EUR][1000 genomes]
rs57256097	0.84[EUR][1000 genomes]
rs60901740	0.82[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs61175766	0.82[EUR][1000 genomes]
rs6595764	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6595767	0.85[CEU][hapmap];0.86[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];0.86[MEX][hapmap];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6595769	0.85[CEU][hapmap];0.86[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];0.86[MEX][hapmap];0.80[TSI][hapmap];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6595773	0.82[YRI][hapmap]
rs67200948	0.96[ASN][1000 genomes]
rs67854568	0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs68035691	0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6874392	0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6874521	0.85[CEU][hapmap];1.00[CHB][hapmap];0.93[ASN][1000 genomes]
rs6874752	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6881894	1.00[CEU][hapmap];0.81[CHD][hapmap];0.97[GIH][hapmap]
rs6882034	0.82[EUR][1000 genomes]
rs6883445	0.90[YRI][hapmap]
rs6888010	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6891785	0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6897163	0.90[YRI][hapmap]
rs6897290	0.92[ASN][1000 genomes]
rs72790405	0.83[EUR][1000 genomes]
rs72790408	0.83[EUR][1000 genomes]
rs72790410	0.83[EUR][1000 genomes]
rs72790411	0.83[EUR][1000 genomes]
rs72790412	0.83[EUR][1000 genomes]
rs72790418	0.84[EUR][1000 genomes]
rs72790419	0.84[EUR][1000 genomes]
rs72790422	1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72790424	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72790426	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72790428	0.84[EUR][1000 genomes]
rs72790430	0.84[EUR][1000 genomes]
rs72790433	0.84[EUR][1000 genomes]
rs72790438	0.84[EUR][1000 genomes]
rs72790444	0.84[EUR][1000 genomes]
rs72790451	0.84[EUR][1000 genomes]
rs72790460	0.82[EUR][1000 genomes]
rs72790468	0.81[EUR][1000 genomes]
rs72790470	0.81[EUR][1000 genomes]
rs72790475	0.81[EUR][1000 genomes]
rs73786108	0.82[EUR][1000 genomes]
rs7700469	0.81[EUR][1000 genomes]
rs7730171	0.83[EUR][1000 genomes]
rs7731380	0.81[EUR][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
rs11950427	SLC12A2	cis	cerebellum	SCAN

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:126742800-126782000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr5:126742800-126792400	Weak transcription	HUES64 Cell Line	embryonic stem cell
3	chr5:126743000-126784800	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr5:126755400-126774400	Weak transcription	Skeletal Muscle Female	skeletal muscle
5	chr5:126756000-126770400	Weak transcription	Fetal Muscle Trunk	muscle
6	chr5:126759200-126774000	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr5:126760400-126778600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
8	chr5:126761000-126774800	Weak transcription	HUES48 Cell Line	embryonic stem cell
9	chr5:126761000-126783400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
10	chr5:126761600-126774000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
11	chr5:126761800-126776600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr5:126761800-126779600	Weak transcription	Right Atrium	heart
13	chr5:126762800-126769200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr5:126762800-126778400	Weak transcription	Pancreas	Pancrea
15	chr5:126763000-126770000	Enhancers	Cortex derived primary cultured neurospheres	brain
16	chr5:126763200-126770600	Enhancers	Brain Substantia Nigra	brain
17	chr5:126763400-126794000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr5:126764600-126770400	Weak transcription	HSMMtube	muscle
19	chr5:126765800-126782000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr5:126766000-126770200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr5:126766000-126770400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr5:126766200-126770400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr5:126767800-126769400	Enhancers	Brain Germinal Matrix	brain
24	chr5:126768000-126769200	Enhancers	Fetal Brain Male	brain
25	chr5:126768000-126773600	Weak transcription	Fetal Muscle Leg	muscle
26	chr5:126768200-126770400	Weak transcription	Brain Cingulate Gyrus	brain
27	chr5:126768200-126770400	Weak transcription	Brain Hippocampus Middle	brain
28	chr5:126768200-126776200	Weak transcription	Brain Inferior Temporal Lobe	brain
29	chr5:126768200-126782000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr5:126768600-126770400	Weak transcription	Brain Angular Gyrus	brain
31	chr5:126768800-126770000	Weak transcription	Fetal Stomach	stomach
32	chr5:126769000-126769200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr5:126769000-126769400	Enhancers	Brain Anterior Caudate	brain
34	chr5:126769000-126769400	Enhancers	Fetal Brain Female	brain

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