Variant report

Variant	rs1249575
Chromosome Location	chr10:28659440-28659441
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 14 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs11007060	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1148199	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1249273	1.00[ASN][1000 genomes]
rs3847383	1.00[CHD][hapmap]
rs7919947	1.00[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv917149	chr10:28018919-28688694	Enhancers Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv1041555	chr10:28419399-29304934	Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
3	nsv1037863	chr10:28419399-29378871	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
4	nsv540521	chr10:28419399-29378871	Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
5	nsv1044938	chr10:28601993-28659440	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	esv1839810	chr10:28656826-28665006	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	nsv550286	chr10:28658275-28664652	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
8	nsv550287	chr10:28658275-28664798	Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
9	nsv550288	chr10:28658275-28665041	Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1249575	SVIL	cis	cerebellum	SCAN
rs1249575	LOC387646	cis	cerebellum	SCAN
rs1249575	MPP7	cis	cerebellum	SCAN

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:28644400-28665000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr10:28654200-28660400	Enhancers	Primary monocytes fromperipheralblood	blood
3	chr10:28655000-28659600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
4	chr10:28656200-28661800	Weak transcription	Colonic Mucosa	Colon
5	chr10:28656800-28659800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
6	chr10:28657200-28659600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
7	chr10:28657200-28660400	Enhancers	Primary T helper naive cells from peripheral blood	blood
8	chr10:28657200-28660400	Enhancers	Monocytes-CD14+_RO01746	blood
9	chr10:28657200-28662600	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr10:28657400-28660000	Enhancers	Primary T helper cells PMA-I stimulated	--
11	chr10:28657600-28659600	Enhancers	Primary T cells fromperipheralblood	blood
12	chr10:28657600-28659600	Enhancers	Primary T helper cells fromperipheralblood	blood
13	chr10:28657800-28659600	Enhancers	Primary T cells from cord blood	blood
14	chr10:28657800-28661400	Weak transcription	Placenta	Placenta
15	chr10:28658000-28659600	Weak transcription	HepG2	liver
16	chr10:28658600-28660800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr10:28659400-28664400	Weak transcription	Primary neutrophils fromperipheralblood	blood

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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