Variant report

Variant	rs13405136
Chromosome Location	chr2:231162341-231162342
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 21 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs13403849	0.82[ASN][1000 genomes]
rs1559909	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2162480	0.92[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs2303542	0.92[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs34304229	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3754938	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3769845	1.00[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56317957	0.99[ASN][1000 genomes]
rs58989813	0.81[ASN][1000 genomes]
rs6708227	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6717938	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6734941	0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs730010	0.80[ASN][1000 genomes]
rs7557737	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs7582543	0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1001562	chr2:230862717-231187043	Flanking Active TSS ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Active TSS Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	nsv536156	chr2:230862717-231187043	Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
3	nsv498047	chr2:230951712-231250489	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
4	esv18000	chr2:231072978-231467847	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
5	esv3417154	chr2:231159789-231258938	Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	esv3348338	chr2:231160124-231259498	Weak transcription Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	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
rs13405136	UGT1A1	cis	cerebellum	SCAN
rs13405136	ARMC9	cis	cerebellum	SCAN

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:231090200-231170000	Weak transcription	Spleen	Spleen
2	chr2:231128200-231166000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
3	chr2:231147200-231165400	Strong transcription	Primary T cells fromperipheralblood	blood
4	chr2:231147800-231182400	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr2:231153000-231165400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
6	chr2:231153400-231165400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr2:231153800-231183400	Weak transcription	Duodenum Mucosa	Duodenum
8	chr2:231154000-231165400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr2:231154600-231164400	Strong transcription	Primary T helper memory cells from peripheral blood 2	blood
10	chr2:231158400-231165400	Strong transcription	Primary T cells from cord blood	blood
11	chr2:231158400-231165800	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
12	chr2:231159600-231165000	ZNF genes & repeats	GM12878-XiMat	blood
13	chr2:231161400-231162600	Strong transcription	Primary T killer memory cells from peripheral blood	blood
14	chr2:231161400-231165000	Strong transcription	Primary B cells from cord blood	blood
15	chr2:231161600-231165200	Strong transcription	Primary T helper cells PMA-I stimulated	--
16	chr2:231161600-231165400	Strong transcription	Primary T helper naive cells from peripheral blood	blood
17	chr2:231161600-231166200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr2:231161600-231173800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
19	chr2:231161800-231165400	Strong transcription	Primary T helper cells fromperipheralblood	blood
20	chr2:231161800-231165400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
21	chr2:231162200-231166000	Strong transcription	Primary B cells from peripheral blood	blood

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