Variant report

Variant	rs10887778
Chromosome Location	chr10:89853442-89853443
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	chr10:89851904..89854023-chr10:89865175..89867253,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PTEN-7	chr10:89853303-89853509	NONHSAT015467

Extended variants
information (count: 13 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs10159513	0.86[CHB][hapmap];0.94[JPT][hapmap]
rs10159903	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10160109	0.96[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs10788581	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10788583	0.88[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs10887779	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10887780	0.90[CHB][hapmap];0.94[JPT][hapmap]
rs10887783	0.81[AMR][1000 genomes]
rs11202655	0.90[ASW][hapmap];0.85[CHB][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs11202656	0.86[CHB][hapmap];0.94[JPT][hapmap];0.88[MEX][hapmap];0.86[AMR][1000 genomes]
rs17108932	0.81[CHB][hapmap];0.88[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv831940	chr10:89811247-89989199	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	esv3387445	chr10:89851072-89855170	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10887778	PAPSS2	cis	cerebellum	SCAN
rs10887778	UNC13B	trans	lymphoblastoid	seeQTL

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:89839400-89855000	Weak transcription	Lung	lung
2	chr10:89848800-89856200	Enhancers	Fetal Thymus	thymus
3	chr10:89849400-89854200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
4	chr10:89849400-89854600	Enhancers	Primary monocytes fromperipheralblood	blood
5	chr10:89849600-89853600	Enhancers	Primary T killer memory cells from peripheral blood	blood
6	chr10:89850200-89854200	Enhancers	Primary T cells fromperipheralblood	blood
7	chr10:89850400-89854600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
8	chr10:89851800-89853600	Enhancers	Monocytes-CD14+_RO01746	blood
9	chr10:89851800-89857400	Enhancers	Dnd41	blood
10	chr10:89852000-89854800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr10:89852200-89855400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
12	chr10:89852400-89853800	Enhancers	Adipose Nuclei	Adipose
13	chr10:89852400-89853800	Enhancers	GM12878-XiMat	blood
14	chr10:89852400-89854400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr10:89852400-89855200	Weak transcription	Pancreatic Islets	Pancreatic Islet
16	chr10:89852600-89855000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr10:89852600-89855400	Weak transcription	Thymus	Thymus
18	chr10:89852800-89854200	Weak transcription	HMEC	breast
19	chr10:89852800-89854800	Weak transcription	Rectal Mucosa Donor 29	rectum
20	chr10:89853000-89854600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr10:89853000-89854600	Weak transcription	NHEK	skin
22	chr10:89853000-89854800	Weak transcription	Fetal Lung	lung
23	chr10:89853000-89857200	Weak transcription	Skeletal Muscle Female	skeletal muscle
24	chr10:89853200-89854400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
25	chr10:89853200-89854600	Weak transcription	Liver	Liver
26	chr10:89853200-89855000	Weak transcription	Fetal Intestine Large	intestine
27	chr10:89853400-89853800	Enhancers	Primary neutrophils fromperipheralblood	blood
28	chr10:89853400-89854800	Weak transcription	Left Ventricle	heart
29	chr10:89853400-89854800	Weak transcription	Pancreas	Pancrea
30	chr10:89853400-89857200	Weak transcription	Fetal Heart	heart
31	chr10:89853400-89857800	Weak transcription	Primary B cells from cord blood	blood

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