Variant report

Variant	rs2237979
Chromosome Location	chr11:17461543-17461544
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOXA2	chr11:17460751-17461741	HepG2	liver:	n/a	n/a
2	TCF12	chr11:17460798-17461640	A549	lung:	n/a	chr11:17461207-17461216
3	FOXA2	chr11:17460781-17461554	A549	lung:	n/a	n/a
4	SIN3AK20	chr11:17460782-17461574	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:17459219..17462653-chr11:17463041..17467220,4	K562	blood:

Variant related genes	Relation type
SDHCP4	TF binding region
ENSG00000006071	Chromatin interaction

Extended variants
information (count: 73 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs10766399	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10766400	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10832788	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10832789	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10832791	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11024290	0.84[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.82[MEX][hapmap];0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11024296	0.95[CEU][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11024297	0.89[EUR][1000 genomes]
rs11024299	0.91[CEU][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11821723	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11826760	0.96[CEU][hapmap];0.95[MEX][hapmap];0.87[TSI][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12285976	0.96[CEU][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12417170	0.84[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.93[JPT][hapmap];0.86[MEX][hapmap];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12786125	0.86[ASN][1000 genomes]
rs12794627	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17775256	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2040653	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.85[TSI][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2073585	0.82[MEX][hapmap]
rs2073586	0.90[MEX][hapmap];0.80[EUR][1000 genomes]
rs2073587	0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2074319	0.90[EUR][1000 genomes]
rs2237966	0.91[CEU][hapmap];0.95[MEX][hapmap];0.85[TSI][hapmap];0.89[EUR][1000 genomes]
rs2237968	0.81[CEU][hapmap];0.89[EUR][1000 genomes]
rs2237969	0.89[EUR][1000 genomes]
rs2237970	0.89[EUR][1000 genomes]
rs2237971	0.91[CEU][hapmap];0.88[EUR][1000 genomes]
rs2237973	0.83[AMR][1000 genomes]
rs2237974	0.95[CEU][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2237975	0.91[CEU][hapmap];0.91[EUR][1000 genomes]
rs2237976	0.81[CEU][hapmap]
rs2237978	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2237980	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2237981	0.84[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.93[JPT][hapmap];0.86[MEX][hapmap]
rs2237982	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[JPT][hapmap];0.86[MEX][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2237983	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2283254	0.91[CEU][hapmap];0.95[MEX][hapmap];0.83[TSI][hapmap];0.89[EUR][1000 genomes]
rs2283256	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2283258	0.83[CEU][hapmap];0.81[MEX][hapmap]
rs2283261	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3781950	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3815066	0.90[EUR][1000 genomes]
rs3819518	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3819520	0.96[CEU][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3819521	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3819522	0.96[CEU][hapmap];0.89[EUR][1000 genomes]
rs3819523	0.95[CEU][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3819524	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4148601	0.91[CEU][hapmap];0.88[EUR][1000 genomes]
rs4148602	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4148604	0.95[CEU][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4148605	0.87[EUR][1000 genomes]
rs4148607	0.95[CEU][hapmap];0.87[EUR][1000 genomes]
rs4148608	0.88[EUR][1000 genomes]
rs4148609	0.95[CEU][hapmap];0.90[EUR][1000 genomes]
rs4148610	0.96[CEU][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4459286	0.84[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.93[JPT][hapmap];0.86[MEX][hapmap];0.96[ASN][1000 genomes]
rs6486370	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs7105391	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs7105832	0.96[CEU][hapmap];0.95[MEX][hapmap];0.87[TSI][hapmap];0.92[EUR][1000 genomes]
rs7106250	0.91[CEU][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7117162	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.88[TSI][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7119716	0.92[EUR][1000 genomes]
rs7120682	0.92[EUR][1000 genomes]
rs71457878	0.81[EUR][1000 genomes]
rs757109	0.84[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.93[JPT][hapmap];0.86[MEX][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7932043	0.82[ASN][1000 genomes]
rs7934185	0.96[ASN][1000 genomes]
rs7943461	0.96[CEU][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7947326	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7950189	0.80[CHB][hapmap];0.82[ASN][1000 genomes]
rs886291	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs886292	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv469895	chr11:17368270-17584220	Weak transcription Bivalent Enhancer Genic enhancers Enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2237979	PDE3B	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:17443800-17462600	Weak transcription	Brain Substantia Nigra	brain
2	chr11:17454000-17464000	Weak transcription	Brain Anterior Caudate	brain
3	chr11:17454200-17465800	Weak transcription	Brain Angular Gyrus	brain
4	chr11:17456000-17469200	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr11:17457000-17467200	Weak transcription	Fetal Brain Male	brain
6	chr11:17457200-17465400	Weak transcription	Cortex derived primary cultured neurospheres	brain
7	chr11:17457400-17464600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr11:17458800-17462000	Enhancers	Fetal Thymus	thymus
9	chr11:17460000-17461600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr11:17460200-17462400	Strong transcription	Fetal Brain Female	brain
11	chr11:17460400-17461600	Enhancers	Fetal Lung	lung
12	chr11:17460400-17462200	Enhancers	A549	lung
13	chr11:17460600-17461600	Enhancers	Fetal Intestine Small	intestine
14	chr11:17460800-17461800	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
15	chr11:17460800-17461800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr11:17460800-17462000	Weak transcription	Pancreatic Islets	Pancreatic Islet
17	chr11:17460800-17474000	Weak transcription	Brain Cingulate Gyrus	brain
18	chr11:17461000-17461600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
19	chr11:17461200-17461600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr11:17461200-17461600	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
21	chr11:17461200-17461800	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
22	chr11:17461200-17497400	Weak transcription	Gastric	stomach
23	chr11:17461400-17461800	Bivalent Enhancer	Stomach Mucosa	stomach
24	chr11:17461400-17462400	Weak transcription	Dnd41	blood

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