Variant report

Variant	rs786399
Chromosome Location	chr10:28605526-28605527
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 35 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10826432	0.82[CHB][hapmap]
rs11006935	1.00[CHB][hapmap]
rs11006941	1.00[CHB][hapmap]
rs11006942	1.00[CHB][hapmap]
rs11006948	1.00[CHB][hapmap]
rs11006971	1.00[CHB][hapmap]
rs1148182	0.82[CHB][hapmap];0.85[JPT][hapmap];0.87[LWK][hapmap];0.81[MKK][hapmap];0.80[ASN][1000 genomes]
rs1148183	0.82[CHB][hapmap];0.82[JPT][hapmap];0.86[YRI][hapmap];0.83[AFR][1000 genomes]
rs1148185	0.82[CHB][hapmap];0.85[JPT][hapmap];0.91[LWK][hapmap];0.80[MKK][hapmap];0.86[YRI][hapmap];0.83[AFR][1000 genomes]
rs1148186	0.82[JPT][hapmap];0.85[YRI][hapmap];0.83[AFR][1000 genomes]
rs12254745	1.00[CHB][hapmap]
rs12358648	1.00[CHB][hapmap]
rs1418758	0.82[CHB][hapmap]
rs16928633	1.00[CHB][hapmap]
rs2100614	0.82[CHB][hapmap]
rs2616615	0.82[ASN][1000 genomes]
rs703015	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs703016	0.89[ASN][1000 genomes]
rs703017	0.89[ASN][1000 genomes]
rs7070175	1.00[CHB][hapmap]
rs7073107	0.82[CHB][hapmap]
rs7078271	1.00[CHB][hapmap]
rs7100335	1.00[CHB][hapmap]
rs72805609	0.80[ASN][1000 genomes]
rs786392	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs786397	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7898888	0.85[JPT][hapmap]
rs7911615	1.00[CHB][hapmap]
rs7916525	1.00[CHB][hapmap]
rs813081	0.84[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs786399	C8orf41	trans	cerebellum	SCAN
rs786399	MPP7	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:28592800-28606600	Weak transcription	Colon Smooth Muscle	Colon
2	chr10:28593000-28607600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
3	chr10:28593200-28605800	Weak transcription	Primary T cells fromperipheralblood	blood
4	chr10:28593200-28615400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr10:28593400-28613400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
6	chr10:28593400-28615200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
7	chr10:28594000-28606600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr10:28596800-28618800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
9	chr10:28597200-28611000	Weak transcription	Pancreas	Pancrea
10	chr10:28597400-28606200	Weak transcription	Primary T helper cells fromperipheralblood	blood
11	chr10:28597400-28614000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
12	chr10:28597600-28613800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
13	chr10:28601600-28615400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr10:28602000-28605800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr10:28602000-28615200	Weak transcription	Primary T helper cells PMA-I stimulated	--
16	chr10:28604000-28615600	Weak transcription	Primary T cells from cord blood	blood
17	chr10:28605400-28605800	Active TSS	Monocytes-CD14+_RO01746	blood

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