Variant report

Variant	rs2089088
Chromosome Location	chr1:160586587-160586588
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:160583254..160585233-chr1:160585992..160588888,2	K562	blood:

Extended variants
information (count: 33 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs1061217	0.83[CHD][hapmap];0.86[JPT][hapmap];0.89[ASN][1000 genomes]
rs10752638	0.89[ASN][1000 genomes]
rs10797083	0.88[ASN][1000 genomes]
rs10908789	0.82[ASN][1000 genomes]
rs10908794	0.88[ASN][1000 genomes]
rs10908796	0.89[ASN][1000 genomes]
rs11265442	0.80[JPT][hapmap];0.83[ASN][1000 genomes]
rs11265444	0.85[ASN][1000 genomes]
rs11265449	0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11265451	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12046687	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12048466	0.84[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.91[TSI][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12402879	0.80[JPT][hapmap];0.80[ASN][1000 genomes]
rs12736781	0.82[ASN][1000 genomes]
rs1394079	0.96[CEU][hapmap];0.81[CHB][hapmap];0.90[JPT][hapmap];0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1572382	0.80[JPT][hapmap]
rs1604783	0.88[ASN][1000 genomes]
rs164283	0.92[CEU][hapmap]
rs2102225	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2102226	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2369725	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2369726	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6427535	0.89[ASN][1000 genomes]
rs6668760	0.81[CHD][hapmap];0.80[JPT][hapmap];0.80[ASN][1000 genomes]
rs6692382	0.81[CHD][hapmap];0.80[JPT][hapmap];0.80[ASN][1000 genomes]
rs7526815	0.90[ASN][1000 genomes]
rs7534679	0.80[ASN][1000 genomes]
rs927202	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs977019	0.81[CHD][hapmap];0.80[JPT][hapmap]

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	esv1829614	chr1:160465291-160595000	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	nsv831703	chr1:160496124-160643024	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	esv1822379	chr1:160545332-160831143	Enhancers Active TSS Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
4	nsv831714	chr1:160581168-160776809	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs2089088	TAGLN2	cis	cerebellum	SCAN
rs2089088	TRIM46	cis	cerebellum	SCAN
rs2089088	ADAMTS4	cis	parietal	SCAN
rs2089088	SLAMF6	cis	lymphoblastoid	seeQTL
rs2089088	KCNJ9	cis	parietal	SCAN
rs2089088	VANGL2	cis	cerebellum	SCAN
rs2089088	MNDA	cis	parietal	SCAN

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:160576200-160591400	Weak transcription	Spleen	Spleen
2	chr1:160576800-160591400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
3	chr1:160577000-160590800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
4	chr1:160578000-160587400	Strong transcription	Primary B cells from peripheral blood	blood
5	chr1:160579000-160589400	Strong transcription	GM12878-XiMat	blood
6	chr1:160579800-160593200	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr1:160582200-160591800	Genic enhancers	Primary T helper cells PMA-I stimulated	--
8	chr1:160584400-160589800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr1:160584400-160594600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr1:160584600-160587600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
11	chr1:160584800-160587400	Strong transcription	Fetal Thymus	thymus
12	chr1:160584800-160591400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr1:160585200-160586600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr1:160585200-160587600	Strong transcription	Primary T cells fromperipheralblood	blood
15	chr1:160585200-160592400	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
16	chr1:160585400-160586600	Genic enhancers	Primary T helper memory cells from peripheral blood 1	blood
17	chr1:160585400-160589800	Genic enhancers	Primary T helper memory cells from peripheral blood 2	blood
18	chr1:160585600-160594800	Weak transcription	K562	blood
19	chr1:160585800-160586800	Strong transcription	Primary T helper cells fromperipheralblood	blood
20	chr1:160585800-160588000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
21	chr1:160585800-160588000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
22	chr1:160586000-160588200	Weak transcription	Primary B cells from cord blood	blood
23	chr1:160586000-160588800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
24	chr1:160586000-160588800	Strong transcription	Thymus	Thymus
25	chr1:160586200-160587000	Weak transcription	Primary T cells from cord blood	blood

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