Variant report

Variant	rs12233927
Chromosome Location	chr5:126737444-126737445
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:126732573..126736586-chr5:126737004..126738980,3	K562	blood:

Extended variants
information (count: 91 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:85)

rs_ID	r²[population]
rs10519936	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.96[TSI][hapmap];0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10519937	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs10519938	1.00[CEU][hapmap];0.97[GIH][hapmap];0.85[TSI][hapmap];0.86[EUR][1000 genomes]
rs11743934	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11949330	0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11949373	0.85[EUR][1000 genomes]
rs11950058	0.85[EUR][1000 genomes]
rs11950427	1.00[CEU][hapmap];0.97[GIH][hapmap];0.88[MEX][hapmap];0.82[YRI][hapmap]
rs11952366	0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11952552	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11952947	0.85[EUR][1000 genomes]
rs11953024	0.85[EUR][1000 genomes]
rs11958435	0.85[EUR][1000 genomes]
rs11959505	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs12234066	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1363385	0.86[EUR][1000 genomes]
rs1363388	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.86[LWK][hapmap];0.90[MKK][hapmap];0.96[TSI][hapmap];0.95[EUR][1000 genomes]
rs1363631	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1422318	1.00[CEU][hapmap];0.90[JPT][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1529467	0.85[EUR][1000 genomes]
rs1593949	0.90[EUR][1000 genomes]
rs1593950	0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs17164902	0.82[EUR][1000 genomes]
rs17164903	0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs17164915	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17164935	0.85[CEU][hapmap];0.93[TSI][hapmap]
rs17164951	0.86[YRI][hapmap]
rs17164957	0.82[YRI][hapmap]
rs17164979	0.85[EUR][1000 genomes]
rs17164995	0.94[ASW][hapmap];0.85[CEU][hapmap];0.94[GIH][hapmap];0.91[JPT][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17164996	0.85[CEU][hapmap];0.97[GIH][hapmap];0.82[TSI][hapmap];0.85[EUR][1000 genomes]
rs17165090	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs173509	0.83[EUR][1000 genomes]
rs17444885	0.85[CEU][hapmap]
rs17604615	0.85[CEU][hapmap]
rs17604665	0.85[CEU][hapmap]
rs17604882	0.85[CEU][hapmap]
rs17604889	0.85[CEU][hapmap]
rs17604946	0.85[CEU][hapmap]
rs17673474	0.85[CEU][hapmap]
rs17673517	0.85[CEU][hapmap]
rs17673685	0.85[CEU][hapmap]
rs17839693	1.00[CEU][hapmap];0.83[JPT][hapmap];0.95[YRI][hapmap];0.90[AFR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17839695	0.85[CEU][hapmap];0.86[EUR][1000 genomes]
rs2173978	0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2408871	1.00[CEU][hapmap];0.97[GIH][hapmap];0.88[MEX][hapmap]
rs2408873	0.88[EUR][1000 genomes]
rs2434620	0.89[EUR][1000 genomes]
rs2898044	0.83[EUR][1000 genomes]
rs3756721	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3812055	0.85[CEU][hapmap];0.97[GIH][hapmap];0.85[TSI][hapmap];0.86[EUR][1000 genomes]
rs3844184	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3851469	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.91[YRI][hapmap];0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3909351	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs4395678	0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4563674	0.85[EUR][1000 genomes]
rs4604231	0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4637594	0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs55663031	0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs55763657	0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs56006993	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57411417	0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs59745967	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60153933	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60901740	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61175766	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6595764	0.86[EUR][1000 genomes]
rs6595765	0.81[EUR][1000 genomes]
rs6595767	0.82[ASW][hapmap];0.85[CEU][hapmap];0.97[GIH][hapmap];0.81[LWK][hapmap];0.85[TSI][hapmap];0.83[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs6595769	0.82[ASW][hapmap];0.85[CEU][hapmap];0.97[GIH][hapmap];0.81[LWK][hapmap];0.85[TSI][hapmap];0.83[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs67200948	0.84[EUR][1000 genomes]
rs67425941	0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs67854568	0.85[EUR][1000 genomes]
rs68035691	0.85[EUR][1000 genomes]
rs6874392	0.85[EUR][1000 genomes]
rs6874521	0.85[CEU][hapmap];0.91[JPT][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6881894	1.00[CEU][hapmap];1.00[GIH][hapmap];0.96[TSI][hapmap];0.95[EUR][1000 genomes]
rs6883445	0.82[YRI][hapmap]
rs6886487	0.92[EUR][1000 genomes]
rs6888010	0.86[EUR][1000 genomes]
rs6891785	0.85[EUR][1000 genomes]
rs6897163	0.82[YRI][hapmap]
rs6897290	0.82[EUR][1000 genomes]
rs72790443	0.85[EUR][1000 genomes]
rs7700469	0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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
6	nsv526333	chr5:126732427-126746277	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12233927	SLC12A2	cis	cerebellum	SCAN
rs12233927	PRRC1	cis	cerebellum	SCAN

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:126691000-126746000	Weak transcription	Fetal Muscle Trunk	muscle
2	chr5:126710200-126741200	Weak transcription	HUES64 Cell Line	embryonic stem cell
3	chr5:126720000-126742000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr5:126731800-126741800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr5:126731800-126742000	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr5:126732000-126741200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
7	chr5:126732400-126741600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr5:126732600-126741800	Weak transcription	H1 Cell Line	embryonic stem cell
9	chr5:126733200-126739400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr5:126734800-126753400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
11	chr5:126735600-126737600	Enhancers	Primary hematopoietic stem cells	blood
12	chr5:126735600-126737600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr5:126735600-126737800	Enhancers	Primary hematopoietic stem cells short term culture	blood
14	chr5:126735600-126738400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr5:126735800-126737800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr5:126736000-126737600	Enhancers	HSMM	muscle
17	chr5:126736000-126737600	Enhancers	NH-A	brain
18	chr5:126736200-126738600	Enhancers	Cortex derived primary cultured neurospheres	brain
19	chr5:126736200-126741600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
20	chr5:126736600-126737600	Enhancers	Brain Inferior Temporal Lobe	brain
21	chr5:126736600-126737800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
22	chr5:126736800-126738200	Enhancers	Brain Substantia Nigra	brain
23	chr5:126736800-126738400	Enhancers	Brain Hippocampus Middle	brain
24	chr5:126737000-126737600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr5:126737000-126742000	Weak transcription	Fetal Muscle Leg	muscle
26	chr5:126737200-126738800	Strong transcription	HUES48 Cell Line	embryonic stem cell
27	chr5:126737200-126741600	Weak transcription	Brain Anterior Caudate	brain
28	chr5:126737200-126741600	Weak transcription	Brain Cingulate Gyrus	brain
29	chr5:126737200-126741800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr5:126737200-126742000	Weak transcription	Brain Angular Gyrus	brain
31	chr5:126737400-126737800	Flanking Active TSS	HSMMtube	muscle
32	chr5:126737400-126738000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr5:126737400-126738800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain

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