Variant report

Variant	rs11654381
Chromosome Location	chr17:33826344-33826345
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 19 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs11080351	1.00[ASW][hapmap];0.93[TSI][hapmap];0.81[EUR][1000 genomes]
rs11657050	1.00[ASN][1000 genomes]
rs12949518	1.00[ASN][1000 genomes]
rs17548596	1.00[ASW][hapmap]
rs17548645	1.00[CHB][hapmap]
rs1838148	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs34410583	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs34658850	1.00[ASN][1000 genomes]
rs35077171	1.00[ASN][1000 genomes]
rs55990593	1.00[ASN][1000 genomes]
rs62078112	1.00[ASN][1000 genomes]
rs72825932	1.00[ASN][1000 genomes]
rs72825958	1.00[ASN][1000 genomes]
rs72828013	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9898870	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1055936	chr17:33327166-33884184	Strong transcription Weak transcription Flanking Active TSS Bivalent/Poised TSS Enhancers Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	112 gene(s)	inside rSNPs	diseases
2	nsv543317	chr17:33327166-33884184	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	112 gene(s)	inside rSNPs	diseases
3	nsv534371	chr17:33456878-34094068	Strong transcription Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	137 gene(s)	inside rSNPs	diseases
4	nsv574741	chr17:33552275-33827134	Bivalent/Poised TSS Active TSS Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	72 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11654381	TMIGD1	cis	parietal	SCAN
rs11654381	CCL4	cis	lymphoblastoid	seeQTL
rs11654381	ZNF830	cis	cerebellum	SCAN

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:33816000-33826400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chr17:33822200-33826600	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
3	chr17:33823000-33830400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
4	chr17:33823400-33828200	Genic enhancers	Primary T cells fromperipheralblood	blood
5	chr17:33823400-33835600	Weak transcription	GM12878-XiMat	blood
6	chr17:33823800-33828600	Weak transcription	Pancreas	Pancrea
7	chr17:33824200-33827200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
8	chr17:33824200-33834800	Weak transcription	Spleen	Spleen
9	chr17:33824400-33827600	Enhancers	Primary T helper cells PMA-I stimulated	--
10	chr17:33824800-33826800	Genic enhancers	Primary T helper cells fromperipheralblood	blood
11	chr17:33824800-33829000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
12	chr17:33825000-33828800	Strong transcription	Dnd41	blood
13	chr17:33825400-33827600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
14	chr17:33825600-33826800	Genic enhancers	Primary T helper memory cells from peripheral blood 2	blood
15	chr17:33825800-33826400	Bivalent Enhancer	Fetal Lung	lung
16	chr17:33826000-33827000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
17	chr17:33826200-33826400	Enhancers	Primary T helper naive cells from peripheral blood	blood
18	chr17:33826200-33827000	Enhancers	Primary T killer memory cells from peripheral blood	blood
19	chr17:33826200-33835000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood

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Input of quick search could be:

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

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