Variant report

Variant	rs17420447
Chromosome Location	chr10:89891695-89891696
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:89868617..89870229-chr10:89891624..89893252,2	K562	blood:
2	chr10:89623345..89624849-chr10:89890140..89891797,2	MCF-7	breast:
3	chr10:89890101..89893895-chr10:89894982..89898353,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000171862	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs1015953	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1360951	0.80[EUR][1000 genomes]
rs17109095	1.00[JPT][hapmap]
rs17109156	0.88[CHD][hapmap];1.00[JPT][hapmap]
rs17109158	1.00[JPT][hapmap]
rs17109310	0.97[ASN][1000 genomes]
rs17322885	0.81[EUR][1000 genomes]
rs2152533	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4933472	0.81[EUR][1000 genomes]
rs7071618	0.88[ASN][1000 genomes]
rs7095588	0.94[ASN][1000 genomes]
rs7901892	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7902285	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]

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	nsv895877	chr10:89884031-89905498	Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs17420447	LRIT2	cis	parietal	SCAN
rs17420447	LIPJ	cis	cerebellum	SCAN
rs17420447	RGR	cis	parietal	SCAN

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:89878800-89892200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr10:89879200-89896600	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr10:89881200-89903800	Weak transcription	Primary B cells from cord blood	blood
4	chr10:89888800-89891800	Enhancers	Breast Myoepithelial Primary Cells	Breast
5	chr10:89890800-89892400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr10:89890800-89892400	Enhancers	HMEC	breast
7	chr10:89890800-89892400	Enhancers	NHEK	skin
8	chr10:89891000-89892200	Enhancers	Pancreas	Pancrea
9	chr10:89891000-89892600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr10:89891000-89892600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr10:89891200-89891800	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
12	chr10:89891200-89892000	Enhancers	Adipose Nuclei	Adipose
13	chr10:89891400-89891800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
14	chr10:89891400-89891800	Enhancers	Left Ventricle	heart
15	chr10:89891400-89892000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr10:89891400-89892000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr10:89891400-89892200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr10:89891400-89892200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr10:89891400-89892200	Enhancers	Colon Smooth Muscle	Colon
20	chr10:89891400-89892200	Enhancers	Psoas Muscle	Psoas
21	chr10:89891600-89891800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr10:89891600-89892200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr10:89891600-89892400	Enhancers	Gastric	stomach
24	chr10:89891600-89892400	Enhancers	NHLF	lung
25	chr10:89891600-89892600	Active TSS	Skeletal Muscle Male	skeletal muscle

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