Variant report

Variant	rs4680263
Chromosome Location	chr3:150956925-150956926
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:150952073..150954804-chr3:150956645..150959268,2	K562	blood:

Variant related genes	Relation type
ENSG00000266798	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10513391	1.00[CHD][hapmap];0.85[GIH][hapmap];0.83[MKK][hapmap];0.81[TSI][hapmap];0.81[EUR][1000 genomes]
rs10935831	0.81[EUR][1000 genomes]
rs10935832	0.81[EUR][1000 genomes]
rs10935833	0.81[EUR][1000 genomes]
rs10935835	0.96[CHD][hapmap];0.85[GIH][hapmap]
rs11925037	0.85[CHB][hapmap]
rs11926145	0.92[CHD][hapmap];0.85[GIH][hapmap]
rs12107539	0.92[CHD][hapmap];0.81[GIH][hapmap]
rs12497019	0.87[CHD][hapmap];0.81[GIH][hapmap]
rs12636396	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12639390	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16863287	1.00[CHD][hapmap];0.85[GIH][hapmap];0.83[MKK][hapmap];0.81[TSI][hapmap];0.81[EUR][1000 genomes]
rs1882013	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]
rs34997694	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3773621	0.96[CHD][hapmap]
rs4680256	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.94[MEX][hapmap];0.88[MKK][hapmap];0.97[TSI][hapmap];0.91[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4680262	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4680356	0.83[CHD][hapmap];0.81[GIH][hapmap]
rs58139829	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62282985	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6785930	0.92[CHD][hapmap];0.81[GIH][hapmap]
rs7620767	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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	esv2757897	chr3:150791625-150957485	ZNF genes & repeats Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	esv2759188	chr3:150791625-150957485	Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4680263	MED12L	cis	cerebellum	SCAN
rs4680263	SLC33A1	cis	parietal	SCAN
rs4680263	CLRN1	cis	parietal	SCAN
rs4680263	FAM194A	cis	parietal	SCAN

Chromatin state (count:18 , 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	chr3:150946600-150957800	Weak transcription	Gastric	stomach
3	chr3:150946800-150969200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr3:150946800-150983600	Weak transcription	Cortex derived primary cultured neurospheres	brain
5	chr3:150949000-150958400	Weak transcription	Primary hematopoietic stem cells	blood
6	chr3:150949200-150959200	Weak transcription	HUES48 Cell Line	embryonic stem cell
7	chr3:150950000-150966400	Weak transcription	Primary B cells from cord blood	blood
8	chr3:150951200-150957800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr3:150952800-150978400	Weak transcription	Primary neutrophils fromperipheralblood	blood
10	chr3:150953000-150959000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr3:150953200-150957800	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr3:150953600-150959000	Weak transcription	HUES64 Cell Line	embryonic stem cell
13	chr3:150953800-150983800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr3:150954200-150957800	Weak transcription	Fetal Stomach	stomach
15	chr3:150954400-150958200	Weak transcription	Colon Smooth Muscle	Colon
16	chr3:150954600-150958800	Weak transcription	Rectal Smooth Muscle	rectum
17	chr3:150956000-150962200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr3:150956600-150957600	Enhancers	Fetal Lung	lung

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