Variant report

Variant	rs927202
Chromosome Location	chr1:160583364-160583365
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:160582022..160584831-chr1:160612719..160614744,2	K562	blood:
2	chr1:160583254..160585233-chr1:160585992..160588888,2	K562	blood:
3	chr1:160582996..160585216-chr1:160596637..160598593,2	K562	blood:
4	chr1:160577461..160579543-chr1:160581700..160584306,2	K562	blood:

Extended variants
information (count: 33 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs1061217	0.80[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];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11265451	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12046687	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12048466	0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.83[TSI][hapmap];0.87[AMR][1000 genomes];0.91[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];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1572382	0.80[JPT][hapmap]
rs1604783	0.88[ASN][1000 genomes]
rs164283	0.92[CEU][hapmap]
rs2089088	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]
rs2102225	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2102226	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2369725	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2369726	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6427535	0.89[ASN][1000 genomes]
rs6668760	0.80[JPT][hapmap];0.80[ASN][1000 genomes]
rs6692382	0.80[JPT][hapmap];0.80[ASN][1000 genomes]
rs7526815	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7534679	0.80[ASN][1000 genomes]
rs977019	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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs927202	TRIM46	cis	cerebellum	SCAN
rs927202	KCNJ9	cis	parietal	SCAN
rs927202	VANGL2	cis	cerebellum	SCAN

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:160575600-160584000	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
2	chr1:160576200-160591400	Weak transcription	Spleen	Spleen
3	chr1:160576400-160584800	Genic enhancers	Fetal Thymus	thymus
4	chr1:160576800-160591400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
5	chr1:160577000-160584200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr1:160577000-160590800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
7	chr1:160577200-160584400	Genic enhancers	Thymus	Thymus
8	chr1:160577400-160584200	Strong transcription	Primary T cells from cord blood	blood
9	chr1:160577600-160584400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
10	chr1:160578000-160587400	Strong transcription	Primary B cells from peripheral blood	blood
11	chr1:160579000-160584000	Strong transcription	Primary T cells fromperipheralblood	blood
12	chr1:160579000-160589400	Strong transcription	GM12878-XiMat	blood
13	chr1:160579800-160593200	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr1:160580200-160583400	Strong transcription	Primary B cells from cord blood	blood
15	chr1:160580800-160584200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr1:160582200-160591800	Genic enhancers	Primary T helper cells PMA-I stimulated	--
17	chr1:160582800-160584000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
18	chr1:160582800-160584200	Genic enhancers	Primary T helper memory cells from peripheral blood 2	blood
19	chr1:160582800-160584200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
20	chr1:160583000-160583600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
21	chr1:160583000-160583800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
22	chr1:160583200-160584200	Weak transcription	Primary T helper cells fromperipheralblood	blood
23	chr1:160583200-160585200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr1:160583200-160585400	Weak transcription	Primary T helper naive cells from peripheral blood	blood

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