Variant report

Variant	rs4405216
Chromosome Location	chr10:89820170-89820171
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 7 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs1819575	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1819576	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1855970	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1855971	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1855972	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6586117	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 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

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs4405216	MMRN2	cis	parietal	SCAN
rs4405216	PTEN	cis	parietal	SCAN
rs4405216	BTAF1	cis	parietal	SCAN
rs4405216	LIPN	cis	parietal	SCAN
rs4405216	VSIG4	trans	cerebellum	SCAN

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:89802600-89822200	Weak transcription	Aorta	Aorta
2	chr10:89803400-89822000	Weak transcription	Psoas Muscle	Psoas
3	chr10:89818200-89822200	Weak transcription	Rectal Smooth Muscle	rectum
4	chr10:89818600-89820400	Weak transcription	Spleen	Spleen
5	chr10:89818600-89822200	Weak transcription	Pancreas	Pancrea
6	chr10:89818800-89820600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr10:89819000-89822200	Enhancers	Dnd41	blood
8	chr10:89819400-89820800	Weak transcription	Primary monocytes fromperipheralblood	blood
9	chr10:89819400-89821200	Weak transcription	Monocytes-CD14+_RO01746	blood
10	chr10:89819400-89830400	Enhancers	Primary T cells from cord blood	blood
11	chr10:89819800-89820600	Enhancers	Fetal Thymus	thymus
12	chr10:89819800-89820800	Enhancers	Primary T helper naive cells from peripheral blood	blood
13	chr10:89819800-89821000	Enhancers	Primary hematopoietic stem cells short term culture	blood
14	chr10:89819800-89821000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
15	chr10:89819800-89823200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
16	chr10:89819800-89826400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
17	chr10:89819800-89828200	Enhancers	Primary T cells fromperipheralblood	blood
18	chr10:89819800-89832800	Enhancers	Primary B cells from peripheral blood	blood
19	chr10:89820000-89822000	Enhancers	GM12878-XiMat	blood
20	chr10:89820000-89822200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
21	chr10:89820000-89822800	Weak transcription	Sigmoid Colon	Sigmoid Colon
22	chr10:89820000-89826200	Enhancers	Primary T helper cells PMA-I stimulated	--
23	chr10:89820000-89826400	Enhancers	Primary B cells from cord blood	blood

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