Variant report

Variant	rs6594334
Chromosome Location	chr5:108066680-108066681
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RUNX3	chr5:108066305-108066680	GM12878	blood:	n/a	n/a
2	EP300	chr5:108066321-108066706	GM12878	blood:	n/a	chr5:108066490-108066499 chr5:108066489-108066503
3	CEBPB	chr5:108066655-108067022	K562	blood:	n/a	chr5:108066832-108066843
4	BATF	chr5:108066301-108066699	GM12878	blood:	n/a	chr5:108066532-108066543 chr5:108066533-108066543
5	RCOR1	chr5:108066409-108066788	GM12878	blood:	n/a	n/a
6	EBF1	chr5:108066369-108066758	GM12878	blood:	n/a	n/a
7	SPI1	chr5:108066356-108066684	GM12878	blood:	n/a	chr5:108066494-108066503
8	CEBPB	chr5:108066679-108066995	HepG2	liver:	n/a	chr5:108066832-108066843
9	TCF3	chr5:108066280-108066708	GM12878	blood:	n/a	n/a
10	IRF4	chr5:108066375-108066765	GM12878	blood:	n/a	n/a
11	SPI1	chr5:108066318-108066727	GM12891	blood:	n/a	chr5:108066494-108066503
12	CEBPB	chr5:108066613-108066957	K562	blood:	n/a	chr5:108066832-108066843
13	CEBPB	chr5:108066545-108067015	IMR90	lung:	n/a	chr5:108066832-108066843
14	IRF4	chr5:108066341-108066773	GM12878	blood:	n/a	n/a
15	NFIC	chr5:108066199-108066820	GM12878	blood:	n/a	n/a
16	SPI1	chr5:108066303-108066760	GM12891	blood:	n/a	chr5:108066494-108066503
17	SPI1	chr5:108066054-108066857	GM12878	blood:	n/a	chr5:108066494-108066503
18	NFIC	chr5:108066219-108066903	GM12878	blood:	n/a	n/a
19	GATA2	chr5:108066297-108066929	HUVEC	blood vessel:	n/a	chr5:108066491-108066501 chr5:108066533-108066542
20	RUNX3	chr5:108066260-108066740	GM12878	blood:	n/a	n/a
21	BCL11A	chr5:108066324-108066722	GM12878	blood:	n/a	chr5:108066494-108066503
22	CUX1	chr5:108066364-108066872	GM12878	blood:	n/a	chr5:108066681-108066695
23	FOS	chr5:108066333-108066727	HUVEC	blood vessel:	n/a	chr5:108066533-108066540 chr5:108066492-108066501 chr5:108066532-108066540 chr5:108066530-108066541 chr5:108066583-108066593
24	BATF	chr5:108066377-108066707	GM12878	blood:	n/a	chr5:108066532-108066543 chr5:108066533-108066543

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:108060235..108074407-chr5:108078172..108087811,48	K562	blood:
2	chr5:108059312..108068052-chr5:108079113..108087366,42	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-FER-3	chr5:108065631-108067538	NONHSAT103128

Variant related genes	Relation type
LINC01023	TF binding region
ENSG00000151422	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10038669	0.92[JPT][hapmap]
rs10062204	0.85[JPT][hapmap]
rs10063167	0.92[JPT][hapmap]
rs10073668	0.92[JPT][hapmap]
rs1022045	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs10223256	0.82[AMR][1000 genomes]
rs1109617	0.82[ASW][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11240982	0.81[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.99[ASN][1000 genomes]
rs11739006	0.90[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs12153703	0.82[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs13173714	0.82[ASW][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs13180513	0.92[JPT][hapmap]
rs1423457	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17161476	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2081126	0.92[JPT][hapmap]
rs2081129	0.92[JPT][hapmap]
rs28684578	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2900035	0.92[JPT][hapmap]
rs34660781	0.81[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs35398495	0.96[ASN][1000 genomes]
rs4957789	0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs6594333	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6594336	0.82[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.96[ASN][1000 genomes]
rs6871143	0.82[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs6871239	0.88[ASW][hapmap];0.82[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.99[ASN][1000 genomes]
rs6873068	0.96[ASN][1000 genomes]
rs6874229	0.92[JPT][hapmap]
rs6880284	0.92[JPT][hapmap]
rs6889967	0.82[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs6891194	0.92[JPT][hapmap]
rs6892439	0.99[ASN][1000 genomes]
rs6895027	0.92[JPT][hapmap]
rs7711795	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7712834	0.92[JPT][hapmap]
rs7716320	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.98[ASN][1000 genomes]
rs7716485	0.99[ASN][1000 genomes]
rs7716498	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs7735235	0.92[JPT][hapmap]
rs9285863	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9326748	0.92[JPT][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv882689	chr5:107595383-108299744	Enhancers ZNF genes & repeats Active TSS Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6594334	TMEM232	cis	cerebellum	SCAN

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:108064600-108071600	Weak transcription	Pancreas	Pancrea
2	chr5:108065000-108068400	Enhancers	Primary monocytes fromperipheralblood	blood
3	chr5:108065200-108067400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr5:108065200-108067400	Enhancers	Primary B cells from cord blood	blood
5	chr5:108065200-108068400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr5:108065400-108067200	Enhancers	Monocytes-CD14+_RO01746	blood
7	chr5:108065400-108067400	Enhancers	GM12878-XiMat	blood
8	chr5:108065600-108067000	Enhancers	HUVEC	blood vessel
9	chr5:108066000-108071400	Weak transcription	K562	blood
10	chr5:108066600-108067000	Enhancers	Primary hematopoietic stem cells short term culture	blood
11	chr5:108066600-108082600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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