Variant report

Variant	rs8102488
Chromosome Location	chr19:42190859-42190860
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:42190379..42192601-chr19:42208251..42211218,2	K562	blood:

Variant related genes	Relation type
ENSG00000007306	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs1008577	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10403314	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10407280	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10422983	1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10425592	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12609443	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12609822	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12610950	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1548720	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1548721	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1548722	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1548723	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1548724	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1860329	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2109073	1.00[CHB][hapmap];0.98[CHD][hapmap];0.83[GIH][hapmap];0.90[JPT][hapmap];0.81[TSI][hapmap];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2109074	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2109075	0.82[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.85[GIH][hapmap];0.91[JPT][hapmap];0.91[TSI][hapmap];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2109076	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2215284	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34596329	0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3786868	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3826894	0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4416132	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60613767	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6508990	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs71334987	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7245419	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7250319	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7251886	0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8104755	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8104781	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8113799	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3319146	chr19:42082639-42212929	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	esv3319147	chr19:42082742-42212770	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	esv3422975	chr19:42106166-42212774	Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv522854	chr19:42120283-42931004	Weak transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
5	esv12262	chr19:42186492-42191707	Active TSS Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	nsv442464	chr19:42187340-42191295	Active TSS Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	nsv1061309	chr19:42187716-42228445	Active TSS Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs8102488	KCNJ14	cis	parietal	SCAN
rs8102488	PSG3	cis	multi-tissue	Pritchard
rs8102488	STRN4	cis	cerebellum	SCAN
rs8102488	CEACAM4	cis	multi-tissue	Pritchard
rs8102488	PVR	cis	parietal	SCAN
rs8102488	CEACAM3	cis	multi-tissue	Pritchard
rs8102488	NAPA	cis	parietal	SCAN
rs8102488	PVRL2	cis	parietal	SCAN
rs8102488	SLC6A16	cis	parietal	SCAN
rs8102488	IL4I1	cis	parietal	SCAN

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:42188000-42192600	Active TSS	Rectal Mucosa Donor 29	rectum
2	chr19:42189000-42192200	Active TSS	Rectal Mucosa Donor 31	rectum
3	chr19:42189600-42192200	Active TSS	Colonic Mucosa	Colon

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