Variant report

Variant	rs2638441
Chromosome Location	chr12:21970019-21970020
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 23 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10770860	0.82[ASN][1000 genomes]
rs10841893	0.89[CEU][hapmap]
rs10841894	0.83[ASN][1000 genomes]
rs11046186	0.87[ASN][1000 genomes]
rs11046188	0.82[ASN][1000 genomes]
rs11046191	0.85[ASN][1000 genomes]
rs12821277	0.89[CEU][hapmap];1.00[CHB][hapmap];0.85[ASN][1000 genomes]
rs1283810	0.93[CHB][hapmap];0.86[GIH][hapmap];0.92[MEX][hapmap]
rs1283811	0.93[CHB][hapmap];0.91[YRI][hapmap]
rs1873638	0.93[CHB][hapmap];0.86[GIH][hapmap];0.92[MEX][hapmap]
rs2726120	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs4148679	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.84[MEX][hapmap];0.83[MKK][hapmap];0.91[YRI][hapmap];0.84[AFR][1000 genomes];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7309274	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs829060	1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.86[JPT][hapmap];0.82[LWK][hapmap];0.84[MEX][hapmap];0.81[MKK][hapmap];0.95[ASN][1000 genomes]
rs829061	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs829064	0.82[ASN][1000 genomes]
rs829074	0.93[ASW][hapmap];0.93[CHB][hapmap];0.86[GIH][hapmap];0.92[MEX][hapmap];0.89[MKK][hapmap];0.91[YRI][hapmap]
rs9668454	1.00[CEU][hapmap];0.95[GIH][hapmap];0.80[MEX][hapmap];0.87[TSI][hapmap];0.91[AMR][1000 genomes];0.95[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	nsv1043936	chr12:21562673-21979030	ZNF genes & repeats Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
2	nsv557741	chr12:21578559-22169854	Strong transcription Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
3	nsv1051073	chr12:21910875-22271209	Flanking Bivalent TSS/Enh Weak transcription Active TSS Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
4	nsv470275	chr12:21938544-22126314	Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	esv1803832	chr12:21966362-21972830	Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2638441	PLCZ1	cis	cerebellum	SCAN
rs2638441	ABCC9	cis	parietal	SCAN

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:21953400-21971600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr12:21953800-21981000	Weak transcription	Fetal Muscle Trunk	muscle
3	chr12:21954200-21972200	Weak transcription	Fetal Kidney	kidney
4	chr12:21954400-21980600	Weak transcription	Duodenum Smooth Muscle	Duodenum
5	chr12:21955800-21971600	Weak transcription	Ovary	ovary
6	chr12:21955800-21973600	Weak transcription	Right Ventricle	heart
7	chr12:21957200-21971200	Strong transcription	Skeletal Muscle Female	skeletal muscle
8	chr12:21958200-21981200	Weak transcription	Fetal Muscle Leg	muscle
9	chr12:21958400-21980000	Weak transcription	Stomach Smooth Muscle	stomach
10	chr12:21958400-22003000	Weak transcription	Psoas Muscle	Psoas
11	chr12:21963800-21971800	Weak transcription	Fetal Lung	lung
12	chr12:21965000-21971600	Weak transcription	Skeletal Muscle Male	skeletal muscle
13	chr12:21966000-21973000	Weak transcription	Gastric	stomach
14	chr12:21967400-21971000	Weak transcription	Fetal Heart	heart
15	chr12:21967800-21970400	Enhancers	Liver	Liver
16	chr12:21968800-21970400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr12:21968800-21971600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr12:21968800-21971600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr12:21968800-21971800	Weak transcription	Muscle Satellite Cultured Cells	--
20	chr12:21968800-21972000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr12:21968800-21978800	Weak transcription	Adipose Nuclei	Adipose
22	chr12:21968800-21978800	Weak transcription	Pancreatic Islets	Pancreatic Islet
23	chr12:21969000-21971200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr12:21969000-21971400	Weak transcription	Osteobl	bone
25	chr12:21969400-21971000	Strong transcription	Left Ventricle	heart
26	chr12:21969400-21971600	Weak transcription	Colon Smooth Muscle	Colon

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