Variant report

Variant	rs2270095
Chromosome Location	chr19:38840896-38840897
allele	C/T
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	POLR2A	chr19:38840849-38841179	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:38834987..38838242-chr19:38838656..38842905,5	MCF-7	breast:
2	chr19:38839437..38845026-chr19:38862738..38867726,6	MCF-7	breast:
3	chr19:38836592..38840441-chr19:38840696..38845039,4	K562	blood:

Variant related genes	Relation type
CATSPERG	TF binding region
ENSG00000238838	TF binding region
ENSG00000099341	Chromatin interaction
ENSG00000238838	Chromatin interaction
ENSG00000099338	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs11666449	0.86[YRI][hapmap]
rs11671779	0.84[CEU][hapmap]
rs11673012	0.84[CEU][hapmap]
rs11673222	0.84[CEU][hapmap]
rs11880532	0.84[CHD][hapmap]
rs11881305	1.00[ASW][hapmap];0.98[GIH][hapmap];0.92[LWK][hapmap];0.94[MKK][hapmap];0.95[TSI][hapmap];0.87[YRI][hapmap];0.85[AFR][1000 genomes]
rs12609247	0.86[CHB][hapmap];0.83[CHD][hapmap];0.86[GIH][hapmap];0.93[LWK][hapmap];0.91[AFR][1000 genomes];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12609878	0.82[CHD][hapmap]
rs12611255	0.88[EUR][1000 genomes]
rs2270094	0.84[CEU][hapmap]
rs2286475	1.00[CEU][hapmap];0.95[GIH][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes]
rs2286476	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.87[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2304176	1.00[CEU][hapmap];0.93[GIH][hapmap];0.97[TSI][hapmap];0.88[EUR][1000 genomes]
rs3178327	0.95[GIH][hapmap];0.86[MKK][hapmap];0.95[TSI][hapmap]
rs3745951	0.84[CEU][hapmap]
rs3815345	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3843754	1.00[ASW][hapmap];0.98[GIH][hapmap];0.97[LWK][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes]
rs4312417	0.86[ASW][hapmap];0.91[GIH][hapmap];0.95[TSI][hapmap]
rs4386247	0.84[CEU][hapmap]
rs4802324	0.86[ASW][hapmap];0.87[TSI][hapmap]
rs4804046	0.84[CEU][hapmap]
rs56849284	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs57618695	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs58728151	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs59898212	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs60071299	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61160177	0.91[EUR][1000 genomes]
rs7252835	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7253960	0.91[EUR][1000 genomes]
rs7257537	0.88[AFR][1000 genomes]
rs7260137	0.84[AFR][1000 genomes]
rs73043010	0.91[AFR][1000 genomes];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs73043037	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8106900	0.88[CEU][hapmap]
rs8112211	1.00[CEU][hapmap];0.98[GIH][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes]
rs931749	0.84[CEU][hapmap]
rs931750	0.84[CEU][hapmap]

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	nsv1063471	chr19:38734744-39148392	Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	73 gene(s)	inside rSNPs	diseases
2	nsv833822	chr19:38760748-38945105	Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	50 gene(s)	inside rSNPs	diseases
3	nsv911658	chr19:38785318-39002140	Genic enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	55 gene(s)	inside rSNPs	diseases
4	nsv470140	chr19:38840139-39119494	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs2270095	LOC390940	cis	parietal	SCAN
rs2270095	C19orf33	cis	normal skin	skin_eQTL
rs2270095	C19orf33	cis	multi-tissue	Pritchard
rs2270095	APOC4	cis	cerebellum	SCAN
rs2270095	PPP1R14A	cis	multi-tissue	Pritchard
rs2270095	PSG4	cis	cerebellum	SCAN
rs2270095	SELV	cis	parietal	SCAN

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38828200-38841400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr19:38828200-38842000	Weak transcription	Brain Angular Gyrus	brain
3	chr19:38828200-38842600	Weak transcription	Esophagus	oesophagus
4	chr19:38828200-38844800	Weak transcription	Brain Substantia Nigra	brain
5	chr19:38828200-38852000	Weak transcription	Right Atrium	heart
6	chr19:38830200-38844800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr19:38834200-38845000	Weak transcription	Spleen	Spleen
8	chr19:38835000-38842600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr19:38835200-38842600	Weak transcription	Fetal Muscle Leg	muscle
10	chr19:38835200-38847000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr19:38835200-38852000	Weak transcription	Pancreas	Pancrea
12	chr19:38836800-38845000	Weak transcription	Brain Cingulate Gyrus	brain
13	chr19:38837400-38842600	Weak transcription	Brain Germinal Matrix	brain
14	chr19:38837400-38842600	Weak transcription	Fetal Muscle Trunk	muscle
15	chr19:38837800-38843000	Weak transcription	Fetal Intestine Small	intestine
16	chr19:38837800-38843800	Weak transcription	Fetal Brain Female	brain
17	chr19:38838200-38841800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
18	chr19:38838200-38843200	Weak transcription	Primary neutrophils fromperipheralblood	blood

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