Variant report

Variant	rs10924841
Chromosome Location	chr1:246968607-246968608
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:19)
CpG islands
(count:0)
Chromatin interactive
region (count:1)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:19 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOXA2	chr1:246968381-246969037	HepG2	liver:	n/a	n/a
2	RFX5	chr1:246968511-246968736	HepG2	liver:	n/a	n/a
3	FOXA1	chr1:246968504-246968984	HepG2	liver:	n/a	n/a
4	BHLHE40	chr1:246968492-246968773	HepG2	liver:	n/a	n/a
5	E2F4	chr1:246968489-246968702	MCF10A-Er-Src	breast:	n/a	n/a
6	MXI1	chr1:246968550-246968756	HepG2	liver:	n/a	n/a
7	MAFF	chr1:246968498-246968858	HepG2	liver:	n/a	n/a
8	FOXA2	chr1:246968531-246969000	A549	lung:	n/a	n/a
9	FOXA2	chr1:246968504-246969041	A549	lung:	n/a	n/a
10	FOXA1	chr1:246968358-246969082	HepG2	liver:	n/a	n/a
11	CEBPB	chr1:246968456-246968815	HepG2	liver:	n/a	n/a
12	MAFK	chr1:246968480-246968856	HepG2	liver:	n/a	n/a
13	MAFK	chr1:246968510-246968851	HepG2	liver:	n/a	n/a
14	FOXA1	chr1:246968535-246968769	T-47D	breast:	n/a	n/a
15	CEBPB	chr1:246968498-246968701	HepG2	liver:	n/a	n/a
16	FOXA1	chr1:246968460-246969056	HepG2	liver:	n/a	n/a
17	FOXA1	chr1:246968382-246969061	HepG2	liver:	n/a	n/a
18	FOXA2	chr1:246968485-246968959	HepG2	liver:	n/a	n/a
19	FOXA1	chr1:246968415-246968878	T-47D	breast:	n/a	n/a

No data

(count:1 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:246966820..246969788-chr1:246972705..246974206,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000252495	TF binding region

Extended variants
information (count: 39 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10924842	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11584835	0.91[EUR][1000 genomes]
rs2996554	0.90[EUR][1000 genomes]
rs2996555	0.91[EUR][1000 genomes]
rs2996557	0.89[EUR][1000 genomes]
rs2996558	0.90[EUR][1000 genomes]
rs3007292	0.91[EUR][1000 genomes]
rs3007293	0.90[EUR][1000 genomes]
rs3007294	0.91[EUR][1000 genomes]
rs35913465	0.91[EUR][1000 genomes]
rs3935608	0.90[CHB][hapmap];0.83[JPT][hapmap]
rs4926465	0.89[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs4926466	0.89[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs4926468	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4926469	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs55829718	0.81[ASN][1000 genomes]
rs55948526	0.91[EUR][1000 genomes]
rs61852556	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6671004	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7515707	0.89[EUR][1000 genomes]
rs7518032	0.89[EUR][1000 genomes]
rs7520180	0.82[ASN][1000 genomes]
rs7524529	0.91[EUR][1000 genomes]
rs7531462	0.91[EUR][1000 genomes]
rs7531476	0.90[EUR][1000 genomes]
rs7531852	0.90[EUR][1000 genomes]
rs7534538	0.91[EUR][1000 genomes]
rs7551504	0.90[ASN][1000 genomes]
rs9426273	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949571	chr1:246688635-247240863	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
2	nsv873421	chr1:246818634-247044692	Weak transcription Strong transcription Bivalent/Poised TSS Bivalent Enhancer Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	esv2762192	chr1:246823857-247069232	Weak transcription Strong transcription ZNF genes & repeats Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
4	nsv1006271	chr1:246832606-247276182	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
5	nsv535416	chr1:246832606-247276182	Strong transcription ZNF genes & repeats Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
6	nsv430413	chr1:246845971-246975015	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
7	nsv873422	chr1:246854862-247002638	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
8	nsv1011346	chr1:246868799-247133898	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
9	nsv999756	chr1:246894542-246969660	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
10	nsv873423	chr1:246923861-246978504	Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Weak transcription Active TSS Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10924841	LOC149134	cis	cerebellum	SCAN
rs10924841	SCCPDH	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:246964400-246973000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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