Variant report

Variant	rs3851469
Chromosome Location	chr5:126746434-126746435
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 78 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs10519936	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10519937	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs10519938	1.00[CEU][hapmap];0.97[GIH][hapmap];0.82[TSI][hapmap];0.81[EUR][1000 genomes]
rs11743934	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11949330	0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11950427	1.00[CEU][hapmap];0.97[GIH][hapmap];0.88[MEX][hapmap];0.90[YRI][hapmap]
rs11952366	0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11952552	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11956397	0.81[YRI][hapmap]
rs11959505	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs12233927	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]
rs12234066	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1363385	0.81[EUR][1000 genomes]
rs1363388	1.00[CEU][hapmap];1.00[GIH][hapmap];0.93[TSI][hapmap];0.89[EUR][1000 genomes]
rs1363631	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][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]
rs1422318	1.00[CEU][hapmap];0.90[JPT][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1593949	0.95[EUR][1000 genomes]
rs1593950	0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs17164902	0.87[EUR][1000 genomes]
rs17164903	0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs17164915	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17164935	0.85[CEU][hapmap];0.89[TSI][hapmap]
rs17164951	0.95[YRI][hapmap]
rs17164956	0.81[YRI][hapmap]
rs17164957	0.90[YRI][hapmap]
rs17164963	0.81[YRI][hapmap]
rs17164995	0.81[ASW][hapmap];0.85[CEU][hapmap];0.94[GIH][hapmap];0.91[JPT][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17164996	0.85[CEU][hapmap];0.97[GIH][hapmap]
rs17165090	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.91[YRI][hapmap];0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][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];0.87[YRI][hapmap];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17839695	0.85[CEU][hapmap];0.81[EUR][1000 genomes]
rs2173978	0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2408871	1.00[CEU][hapmap];0.97[GIH][hapmap];0.88[MEX][hapmap];0.81[TSI][hapmap]
rs2408873	0.93[EUR][1000 genomes]
rs2434620	0.92[EUR][1000 genomes]
rs2898044	0.86[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];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3812055	0.85[CEU][hapmap];0.97[GIH][hapmap];0.82[TSI][hapmap];0.81[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];1.00[TSI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3909351	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs4395678	0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4604231	0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4637594	0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs55663031	0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs55763657	0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs56006993	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57411417	0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs59745967	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60153933	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60901740	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61175766	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6595764	0.81[EUR][1000 genomes]
rs6595767	0.85[CEU][hapmap];0.97[GIH][hapmap];0.81[TSI][hapmap];0.81[EUR][1000 genomes]
rs6595769	0.85[CEU][hapmap];0.97[GIH][hapmap];0.82[TSI][hapmap];0.81[EUR][1000 genomes]
rs6595773	0.82[YRI][hapmap]
rs67425941	0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6874521	0.85[CEU][hapmap];0.91[JPT][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6881894	1.00[CEU][hapmap];1.00[GIH][hapmap];0.93[TSI][hapmap];0.89[EUR][1000 genomes]
rs6883445	0.90[YRI][hapmap]
rs6886487	0.86[EUR][1000 genomes]
rs6888010	0.81[EUR][1000 genomes]
rs6897163	0.90[YRI][hapmap]
rs72790443	0.85[EUR][1000 genomes]
rs7700469	0.94[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3851469	PRRC1	cis	cerebellum	SCAN
rs3851469	SLC12A2	cis	cerebellum	SCAN

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:126734800-126753400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
2	chr5:126742800-126746800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr5:126742800-126754000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr5:126742800-126760200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr5:126742800-126762600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr5:126742800-126782000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr5:126742800-126792400	Weak transcription	HUES64 Cell Line	embryonic stem cell
8	chr5:126743000-126755600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr5:126743000-126784800	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr5:126743400-126760000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
11	chr5:126744400-126746800	Genic enhancers	Fetal Muscle Leg	muscle
12	chr5:126745200-126747000	Weak transcription	Fetal Brain Male	brain
13	chr5:126745600-126748400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
14	chr5:126745800-126746600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr5:126746000-126747000	Strong transcription	iPS-15b Cell Line	embryonic stem cell
16	chr5:126746000-126747000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr5:126746000-126747000	Enhancers	Fetal Stomach	stomach
18	chr5:126746000-126748400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr5:126746000-126749400	Strong transcription	HUES48 Cell Line	embryonic stem cell
20	chr5:126746200-126746600	Strong transcription	Fetal Muscle Trunk	muscle
21	chr5:126746200-126746600	Enhancers	NHDF-Ad	bronchial
22	chr5:126746200-126747000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr5:126746200-126747000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr5:126746200-126747000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr5:126746200-126747200	Strong transcription	H1 Cell Line	embryonic stem cell
26	chr5:126746200-126748000	Strong transcription	Brain Anterior Caudate	brain
27	chr5:126746200-126748800	Strong transcription	HSMMtube	muscle
28	chr5:126746200-126752200	Weak transcription	Brain Cingulate Gyrus	brain
29	chr5:126746200-126754800	Weak transcription	Psoas Muscle	Psoas
30	chr5:126746200-126758000	Weak transcription	HUES6 Cell Line	embryonic stem cell
31	chr5:126746400-126746800	Enhancers	Skeletal Muscle Female	skeletal muscle
32	chr5:126746400-126747200	Enhancers	Primary hematopoietic stem cells short term culture	blood
33	chr5:126746400-126747200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr5:126746400-126747200	Weak transcription	Fetal Lung	lung
35	chr5:126746400-126747400	Enhancers	Primary hematopoietic stem cells	blood
36	chr5:126746400-126747400	Enhancers	GM12878-XiMat	blood
37	chr5:126746400-126752200	Weak transcription	Brain Hippocampus Middle	brain
38	chr5:126746400-126752200	Weak transcription	Brain Substantia Nigra	brain
39	chr5:126746400-126752400	Weak transcription	Cortex derived primary cultured neurospheres	brain
40	chr5:126746400-126752400	Weak transcription	Brain Inferior Temporal Lobe	brain
41	chr5:126746400-126752800	Weak transcription	Brain Angular Gyrus	brain
42	chr5:126746400-126760800	Weak transcription	HSMM	muscle

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