Variant report

Variant	rs1534304
Chromosome Location	chr2:178489264-178489265
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	chr2:178489030..178493776-chr2:178494411..178499893,10	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PDE11A-1	chr2:178487979-178491033	NONHSAT075725

Extended variants
information (count: 47 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10189303	1.00[JPT][hapmap]
rs10469714	1.00[JPT][hapmap]
rs10497493	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs11694988	0.85[CEU][hapmap]
rs12618542	0.86[CEU][hapmap];0.82[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12619506	1.00[JPT][hapmap]
rs12988366	0.85[CEU][hapmap]
rs13000926	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs13010396	0.86[CEU][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs13014512	0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13019660	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs13034886	0.86[CEU][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs13431105	0.85[CEU][hapmap]
rs1405716	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.83[TSI][hapmap];0.92[ASN][1000 genomes]
rs1527398	0.85[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs1527399	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs1527400	1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[MEX][hapmap]
rs1527402	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs1527410	1.00[CHB][hapmap]
rs1544003	1.00[CHB][hapmap]
rs1547580	1.00[CHB][hapmap]
rs1547581	1.00[CHB][hapmap]
rs16865535	0.85[CHD][hapmap]
rs1852530	0.85[CEU][hapmap]
rs1997208	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs1997209	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.92[ASN][1000 genomes]
rs2293471	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap];0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2365619	0.86[CEU][hapmap];0.82[CHB][hapmap];0.90[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes]
rs2886422	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs3731802	1.00[JPT][hapmap]
rs3813257	0.84[ASN][1000 genomes]
rs4893971	0.85[EUR][1000 genomes]
rs4893972	0.86[CEU][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs4893974	0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4893975	0.95[CHD][hapmap]
rs4893976	1.00[CHB][hapmap]
rs6705405	0.86[CEU][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs6730406	1.00[CEU][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6734426	0.86[CEU][hapmap];0.82[CHB][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6734683	0.93[CEU][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs7422544	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs7594290	0.85[CHD][hapmap]

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	nsv999086	chr2:178262348-178773585	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv536055	chr2:178262348-178773585	Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
3	nsv583688	chr2:178427640-178540293	Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
4	nsv583689	chr2:178468008-178509820	Enhancers Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
5	esv1815823	chr2:178479149-178489902	Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1534304	AGPS	cis	cerebellum	SCAN
rs1534304	TTC30B	cis	parietal	SCAN

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:178484000-178499200	Weak transcription	Pancreas	Pancrea
2	chr2:178484200-178490600	Weak transcription	Brain Inferior Temporal Lobe	brain
3	chr2:178484200-178490600	Weak transcription	Fetal Stomach	stomach
4	chr2:178484200-178490800	Weak transcription	Right Atrium	heart
5	chr2:178484400-178490400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr2:178484400-178490600	Weak transcription	HUES6 Cell Line	embryonic stem cell
7	chr2:178484400-178490800	Weak transcription	Adipose Nuclei	Adipose
8	chr2:178484400-178490800	Weak transcription	Colon Smooth Muscle	Colon
9	chr2:178485400-178490600	Weak transcription	HepG2	liver
10	chr2:178487600-178491200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
11	chr2:178487800-178490200	Weak transcription	Fetal Brain Male	brain
12	chr2:178487800-178490600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr2:178487800-178490600	Weak transcription	Brain Angular Gyrus	brain
14	chr2:178487800-178490600	Weak transcription	Brain Cingulate Gyrus	brain
15	chr2:178487800-178490800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr2:178487800-178490800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr2:178487800-178490800	Weak transcription	Brain Anterior Caudate	brain
18	chr2:178487800-178490800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr2:178487800-178491000	Weak transcription	HUES64 Cell Line	embryonic stem cell
20	chr2:178487800-178491200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr2:178488000-178490600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr2:178488000-178490800	Weak transcription	Brain Substantia Nigra	brain
23	chr2:178488000-178490800	Weak transcription	Fetal Brain Female	brain
24	chr2:178488000-178491000	Weak transcription	Brain Germinal Matrix	brain
25	chr2:178488000-178498800	Weak transcription	Fetal Kidney	kidney
26	chr2:178488400-178490000	Weak transcription	HUVEC	blood vessel
27	chr2:178488400-178493400	Weak transcription	Cortex derived primary cultured neurospheres	brain

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