Variant report

Variant	rs2270094
Chromosome Location	chr19:38840139-38840140
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:38834987..38838242-chr19:38838656..38842905,5	MCF-7	breast:
2	chr19:38838273..38840146-chr19:38846615..38848893,2	MCF-7	breast:
3	chr19:38839437..38845026-chr19:38862738..38867726,6	MCF-7	breast:
4	chr19:38836592..38840441-chr19:38840696..38845039,4	K562	blood:

Variant related genes	Relation type
ENSG00000099338	Chromatin interaction
ENSG00000099341	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs11666449	0.89[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.89[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs11668355	0.81[EUR][1000 genomes]
rs11671779	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs11672793	0.95[EUR][1000 genomes]
rs11673012	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs11673222	1.00[CEU][hapmap];0.95[GIH][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes]
rs12459746	0.89[CEU][hapmap];0.83[CHB][hapmap];0.85[CHD][hapmap];0.85[TSI][hapmap];0.80[EUR][1000 genomes]
rs2270093	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2270095	0.84[CEU][hapmap]
rs2286475	0.84[CEU][hapmap]
rs2286476	0.84[CEU][hapmap]
rs2304176	0.84[CEU][hapmap]
rs3745951	1.00[CEU][hapmap];0.95[GIH][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes]
rs3745952	0.93[EUR][1000 genomes]
rs4386247	1.00[CEU][hapmap];0.95[GIH][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes]
rs45437199	0.91[EUR][1000 genomes]
rs4801723	0.82[AMR][1000 genomes]
rs4802351	0.89[ASW][hapmap];0.82[CEU][hapmap]
rs4804046	0.89[ASW][hapmap];1.00[CEU][hapmap];0.95[GIH][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes]
rs57681346	0.81[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs60487067	0.94[AMR][1000 genomes]
rs73041302	0.93[EUR][1000 genomes]
rs8101488	0.93[EUR][1000 genomes]
rs8106900	1.00[CEU][hapmap];0.95[GIH][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes]
rs8112211	0.84[CEU][hapmap]
rs931749	1.00[CEU][hapmap];0.95[GIH][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes]
rs931750	1.00[CEU][hapmap];0.95[GIH][hapmap];0.97[TSI][hapmap];0.93[EUR][1000 genomes]

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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs2270094	C19orf33	cis	normal skin	skin_eQTL
rs2270094	CYP2S1	cis	cerebellum	SCAN
rs2270094	SYCN	cis	parietal	SCAN
rs2270094	SELV	cis	parietal	SCAN
rs2270094	APOC4	cis	cerebellum	SCAN
rs2270094	LOC390940	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38828200-38840400	Weak transcription	Left Ventricle	heart
2	chr19:38828200-38841400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr19:38828200-38842000	Weak transcription	Brain Angular Gyrus	brain
4	chr19:38828200-38842600	Weak transcription	Esophagus	oesophagus
5	chr19:38828200-38844800	Weak transcription	Brain Substantia Nigra	brain
6	chr19:38828200-38852000	Weak transcription	Right Atrium	heart
7	chr19:38830200-38844800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr19:38832200-38840400	Weak transcription	Stomach Smooth Muscle	stomach
9	chr19:38833800-38840400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr19:38834200-38845000	Weak transcription	Spleen	Spleen
11	chr19:38835000-38842600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr19:38835200-38840200	Weak transcription	Brain Hippocampus Middle	brain
13	chr19:38835200-38840200	Weak transcription	Duodenum Mucosa	Duodenum
14	chr19:38835200-38842600	Weak transcription	Fetal Muscle Leg	muscle
15	chr19:38835200-38847000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
16	chr19:38835200-38852000	Weak transcription	Pancreas	Pancrea
17	chr19:38836800-38845000	Weak transcription	Brain Cingulate Gyrus	brain
18	chr19:38837200-38840200	Weak transcription	Cortex derived primary cultured neurospheres	brain
19	chr19:38837400-38842600	Weak transcription	Brain Germinal Matrix	brain
20	chr19:38837400-38842600	Weak transcription	Fetal Muscle Trunk	muscle
21	chr19:38837800-38843000	Weak transcription	Fetal Intestine Small	intestine
22	chr19:38837800-38843800	Weak transcription	Fetal Brain Female	brain
23	chr19:38838200-38841800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
24	chr19:38838200-38843200	Weak transcription	Primary neutrophils fromperipheralblood	blood

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