Variant report

Variant	rs1369517
Chromosome Location	chr2:178946709-178946710
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:178936273..178939016-chr2:178945956..178948361,3	K562	blood:
2	chr2:178940677..178943272-chr2:178945277..178948244,4	K562	blood:
3	chr2:178940297..178942724-chr2:178946031..178947901,2	K562	blood:

Variant related genes	Relation type
ENSG00000128655	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10176475	1.00[CEU][hapmap];0.94[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.82[TSI][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10198111	0.82[CHB][hapmap]
rs10432485	0.94[JPT][hapmap]
rs11886139	0.88[CHB][hapmap];0.94[JPT][hapmap];0.89[ASN][1000 genomes]
rs11887974	0.81[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs11899905	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap]
rs13408924	0.88[CHB][hapmap];0.85[CHD][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs1347441	0.83[CHB][hapmap]
rs1369515	0.81[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.95[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs1435571	0.84[ASW][hapmap];0.93[CEU][hapmap];0.87[GIH][hapmap];0.94[JPT][hapmap];0.96[LWK][hapmap];0.89[MKK][hapmap];0.84[TSI][hapmap];0.94[YRI][hapmap]
rs1852502	0.82[CHD][hapmap]
rs2034255	0.87[ASN][1000 genomes]
rs2163647	1.00[ASW][hapmap];0.88[CHB][hapmap];0.85[CHD][hapmap];0.94[JPT][hapmap];0.83[LWK][hapmap];0.88[YRI][hapmap];0.89[ASN][1000 genomes]
rs2217838	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs4300869	0.84[ASW][hapmap];0.88[CHB][hapmap];0.94[JPT][hapmap];0.88[LWK][hapmap];0.94[YRI][hapmap];0.85[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs56103916	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6433709	0.82[CHB][hapmap]
rs6709343	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs6710329	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6714047	0.94[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs6738461	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap]
rs6740828	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6754705	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs736842	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap]
rs7583491	0.93[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9288014	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][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	nsv533377	chr2:178718801-178963463	Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv875451	chr2:178748294-178953409	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv1009312	chr2:178924318-179215566	Weak transcription Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv536057	chr2:178924318-179215566	Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
5	nsv583739	chr2:178942302-178993562	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1369517	AGPS	cis	parietal	SCAN
rs1369517	PLEKHA3	cis	cerebellum	SCAN
rs1369517	AGPS	cis	lymphoblastoid	seeQTL

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:178946200-178946800	Enhancers	H9 Cell Line	embryonic stem cell
2	chr2:178946200-178946800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived

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