Variant report

Variant	rs12040469
Chromosome Location	chr1:84976810-84976811
allele	C/T
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	SETDB1	chr1:84976200-84977005	U2OS	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:84969735..84979623-chr1:84983174..84994888,16	K562	blood:
2	chr1:84975237..84977774-chr1:85017252..85019567,2	K562	blood:
3	chr1:84966614..84978118-chr1:85034515..85041986,38	K562	blood:

Variant related genes	Relation type
GNG5	TF binding region
ENSG00000117151	Chromatin interaction
ENSG00000122432	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs11163969	0.94[ASN][1000 genomes]
rs11163970	0.94[ASN][1000 genomes]
rs11163979	1.00[ASN][1000 genomes]
rs11163980	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11163981	1.00[ASN][1000 genomes]
rs11163990	0.96[ASN][1000 genomes]
rs11163994	1.00[ASN][1000 genomes]
rs11163999	0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1144276	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12036957	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12071149	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12128801	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12403545	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1246159	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1246236	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1246253	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1246254	0.94[ASN][1000 genomes]
rs1246255	0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1400777	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1533374	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2292191	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2303306	0.81[ASN][1000 genomes]
rs2389743	0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2659173	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2677839	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2794217	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2794218	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2911589	0.81[ASN][1000 genomes]
rs2911593	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2994954	0.89[ASN][1000 genomes]
rs2994955	0.88[ASN][1000 genomes]
rs3021402	0.87[ASN][1000 genomes]
rs312397	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs312401	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4906995	0.94[ASN][1000 genomes]
rs4906997	0.87[ASN][1000 genomes]
rs4907078	0.94[ASN][1000 genomes]
rs6576713	0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6576715	0.82[ASN][1000 genomes]
rs6692765	0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6704211	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7516200	0.92[ASN][1000 genomes]
rs7537818	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9645393	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]

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	nsv830437	chr1:84837524-85001269	Flanking Active TSS Active TSS Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:84973000-84977000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr1:84973000-85003200	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr1:84973200-84982200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr1:84973200-84982200	Weak transcription	NHDF-Ad	bronchial
5	chr1:84973200-85003200	Weak transcription	Adipose Nuclei	Adipose
6	chr1:84973400-84991600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr1:84973400-84993800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr1:84973400-84994400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr1:84973400-84995200	Weak transcription	Primary neutrophils fromperipheralblood	blood
10	chr1:84973400-85002000	Weak transcription	Primary T cells from cord blood	blood
11	chr1:84973600-84984600	Weak transcription	Fetal Heart	heart
12	chr1:84973800-84977200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
13	chr1:84974000-84982200	Weak transcription	Aorta	Aorta
14	chr1:84974200-84991400	Weak transcription	Monocytes-CD14+_RO01746	blood
15	chr1:84975200-85019600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr1:84975800-85030200	Weak transcription	Fetal Intestine Small	intestine

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