Variant report

Variant	rs1920395
Chromosome Location	chr3:150970686-150970687
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	chr3:150965721..150968051-chr3:150969254..150971148,2	K562	blood:

Variant related genes	Relation type
ENSG00000174944	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10212582	1.00[ASN][1000 genomes]
rs11711104	0.89[ASN][1000 genomes]
rs11717955	0.90[CEU][hapmap];0.83[AMR][1000 genomes]
rs12488267	0.83[AFR][1000 genomes]
rs13317873	1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs1882014	0.80[YRI][hapmap]
rs1882016	0.88[YRI][hapmap]
rs1980143	0.90[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs3846072	1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.80[MKK][hapmap];1.00[ASN][1000 genomes]
rs4076581	0.80[TSI][hapmap]
rs4269062	0.84[ASN][1000 genomes]
rs4679772	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs4680254	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs4680257	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs4680260	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs4680273	0.86[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.80[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs6440730	1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs6782715	1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6809692	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs73021201	0.96[ASN][1000 genomes]
rs9815520	1.00[CHB][hapmap];0.91[ASN][1000 genomes]
rs9835328	0.90[CHB][hapmap];0.90[ASN][1000 genomes]
rs9853297	0.95[ASN][1000 genomes]
rs9870740	0.87[YRI][hapmap]
rs9880339	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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
3	esv2754555	chr3:150968302-151054302	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1920395	MED12L	cis	cerebellum	SCAN

Chromatin state (count:20 , 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	chr3:150946800-150983600	Weak transcription	Cortex derived primary cultured neurospheres	brain
3	chr3:150952800-150978400	Weak transcription	Primary neutrophils fromperipheralblood	blood
4	chr3:150953800-150983800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr3:150959600-150977800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr3:150959600-150978200	Weak transcription	Primary hematopoietic stem cells	blood
7	chr3:150961200-150983600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr3:150965000-150980800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
9	chr3:150967000-150971400	Weak transcription	Stomach Smooth Muscle	stomach
10	chr3:150967000-150982600	Weak transcription	Gastric	stomach
11	chr3:150967200-150974200	Weak transcription	Fetal Lung	lung
12	chr3:150967600-150971000	Weak transcription	Fetal Stomach	stomach
13	chr3:150968800-150972000	Weak transcription	Primary B cells from cord blood	blood
14	chr3:150969800-150971400	Enhancers	Stomach Mucosa	stomach
15	chr3:150969800-150977000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr3:150970000-150972200	Weak transcription	Duodenum Smooth Muscle	Duodenum
17	chr3:150970200-150971000	Enhancers	Pancreatic Islets	Pancreatic Islet
18	chr3:150970600-150971400	Enhancers	Rectal Smooth Muscle	rectum
19	chr3:150970600-150972600	Enhancers	Colon Smooth Muscle	Colon
20	chr3:150970600-150974200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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