Variant report

Variant	rs1882013
Chromosome Location	chr3:150967269-150967270
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 30 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10513391	0.82[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];0.88[MKK][hapmap];0.82[ASN][1000 genomes]
rs10935831	0.82[CHB][hapmap];0.82[ASN][1000 genomes]
rs10935832	0.82[CHB][hapmap];0.82[ASN][1000 genomes]
rs10935833	0.82[CHB][hapmap];0.82[ASN][1000 genomes]
rs10935835	0.82[CHB][hapmap];0.96[CHD][hapmap];0.90[GIH][hapmap]
rs11925037	0.85[CHB][hapmap]
rs11926145	0.82[CHB][hapmap];0.92[CHD][hapmap];0.90[GIH][hapmap]
rs12107539	0.92[CHD][hapmap];0.87[GIH][hapmap]
rs12497019	0.87[CHD][hapmap];0.87[GIH][hapmap]
rs12636396	0.86[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12639390	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16863287	0.82[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];0.88[MKK][hapmap];0.82[ASN][1000 genomes]
rs28527299	0.81[ASN][1000 genomes]
rs34997694	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3773621	0.82[CHB][hapmap];0.96[CHD][hapmap];0.81[GIH][hapmap]
rs4680256	1.00[ASW][hapmap];0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.94[TSI][hapmap];0.91[YRI][hapmap];0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4680262	0.89[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4680263	1.00[ASW][hapmap];0.86[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];0.92[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4680307	0.82[CHB][hapmap]
rs4680356	0.83[CHD][hapmap];0.87[GIH][hapmap]
rs58139829	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62282985	0.99[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62282988	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6784934	0.82[CHB][hapmap]
rs6785930	0.92[CHD][hapmap];0.87[GIH][hapmap]
rs7618206	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7620767	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7648875	0.80[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv460894	chr3:150770614-151095093	Enhancers Flanking Bivalent TSS/Enh Weak transcription Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	nsv592045	chr3:150770614-151095093	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1882013	MED12L	cis	cerebellum	SCAN
rs1882013	FAM194A	cis	parietal	SCAN
rs1882013	P2RY13	cis	cerebellum	SCAN
rs1882013	P2RY12	cis	cerebellum	SCAN

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:150946200-150979400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr3:150946800-150969200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr3:150946800-150983600	Weak transcription	Cortex derived primary cultured neurospheres	brain
4	chr3:150952800-150978400	Weak transcription	Primary neutrophils fromperipheralblood	blood
5	chr3:150953800-150983800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr3:150959400-150970600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr3:150959600-150977800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr3:150959600-150978200	Weak transcription	Primary hematopoietic stem cells	blood
9	chr3:150961200-150983600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr3:150965000-150980800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
11	chr3:150966400-150967600	Strong transcription	Primary B cells from cord blood	blood
12	chr3:150966400-150967800	Enhancers	Duodenum Smooth Muscle	Duodenum
13	chr3:150966400-150968000	Enhancers	Fetal Heart	heart
14	chr3:150966400-150970600	Weak transcription	Rectal Smooth Muscle	rectum
15	chr3:150966600-150967400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr3:150966800-150967600	Enhancers	Right Atrium	heart
17	chr3:150967000-150967600	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr3:150967000-150969200	Weak transcription	Stomach Mucosa	stomach
19	chr3:150967000-150971400	Weak transcription	Stomach Smooth Muscle	stomach
20	chr3:150967000-150982600	Weak transcription	Gastric	stomach
21	chr3:150967200-150967600	Enhancers	Fetal Stomach	stomach
22	chr3:150967200-150967800	Enhancers	Colon Smooth Muscle	Colon
23	chr3:150967200-150969400	Enhancers	Pancreatic Islets	Pancreatic Islet
24	chr3:150967200-150974200	Weak transcription	Fetal Lung	lung

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