Variant report

Variant	rs12411830
Chromosome Location	chr10:49487816-49487817
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	IRF4	chr10:49486971-49487900	GM12878	blood:	n/a	n/a
2	POLR2A	chr10:49487706-49488109	GM12878	blood:	n/a	n/a
3	POLR2A	chr10:49487038-49488651	GM12878	blood:	n/a	n/a
4	PAX5	chr10:49487006-49487885	GM12878	blood:	n/a	chr10:49487273-49487292
5	PML	chr10:49486901-49487830	GM12878	blood:	n/a	n/a
6	POLR2A	chr10:49486983-49489175	GM12878	blood:	n/a	n/a
7	ATF2	chr10:49486941-49487901	GM12878	blood:	n/a	n/a
8	POLR2A	chr10:49487016-49487877	GM12892	blood:	n/a	n/a
9	POLR2A	chr10:49487058-49487833	GM12891	blood:	n/a	n/a
10	POLR2A	chr10:49486921-49487946	GM12892	blood:	n/a	n/a
11	POU2F2	chr10:49486969-49487839	GM12878	blood:	n/a	n/a
12	POLR2A	chr10:49486982-49490326	GM12878	blood:	n/a	n/a
13	SP1	chr10:49486997-49487856	GM12878	blood:	n/a	n/a
14	SPI1	chr10:49486878-49488018	GM12878	blood:	n/a	n/a
15	FOXM1	chr10:49486925-49487943	GM12878	blood:	n/a	n/a
16	SP1	chr10:49487504-49487928	GM12878	blood:	n/a	n/a
17	ATF2	chr10:49486865-49488015	GM12878	blood:	n/a	n/a
18	MTA3	chr10:49486897-49487853	GM12878	blood:	n/a	n/a
19	EBF1	chr10:49486992-49487898	GM12878	blood:	n/a	n/a
20	EBF1	chr10:49487002-49487890	GM12878	blood:	n/a	n/a
21	EP300	chr10:49486914-49487902	GM12878	blood:	n/a	n/a
22	CEBPB	chr10:49486912-49487942	GM12878	blood:	n/a	n/a
23	NFIC	chr10:49486804-49487865	GM12878	blood:	n/a	n/a
24	JUND	chr10:49486891-49487938	GM12878	blood:	n/a	n/a
25	POLR2A	chr10:49487095-49487839	GM12892	blood:	n/a	n/a
26	CUX1	chr10:49486994-49487828	GM12878	blood:	n/a	n/a
27	POLR2A	chr10:49486960-49488009	GM12892	blood:	n/a	n/a
28	BATF	chr10:49487504-49487868	GM12878	blood:	n/a	n/a
29	NFIC	chr10:49486890-49487989	GM12878	blood:	n/a	n/a
30	RELA	chr10:49487010-49487922	GM12891	blood:	n/a	n/a
31	RUNX3	chr10:49487026-49488048	GM12878	blood:	n/a	n/a
32	RUNX3	chr10:49486992-49487894	GM12878	blood:	n/a	n/a
33	EBF1	chr10:49486976-49488295	GM12878	blood:	n/a	n/a
34	MEF2A	chr10:49487485-49487884	GM12878	blood:	n/a	n/a
35	RELA	chr10:49487012-49487824	GM12878	blood:	n/a	n/a
36	IRF4	chr10:49487078-49487890	GM12878	blood:	n/a	n/a
37	BCL3	chr10:49486950-49487924	GM12878	blood:	n/a	n/a

Variant related genes	Relation type
FRMPD2	TF binding region

Extended variants
information (count: 46 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10437448	0.83[ASN][1000 genomes]
rs10508901	0.95[JPT][hapmap]
rs10508903	0.90[CHB][hapmap];0.95[JPT][hapmap]
rs10745266	0.89[CHB][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs10745269	0.83[ASN][1000 genomes]
rs10776595	0.90[CHB][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs10776596	0.95[CHB][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs10857560	0.95[CHB][hapmap];0.95[JPT][hapmap]
rs10857561	0.89[JPT][hapmap]
rs11101290	0.81[ASN][1000 genomes]
rs11101318	0.90[CHB][hapmap];0.95[JPT][hapmap]
rs11101320	0.95[CHB][hapmap];0.89[JPT][hapmap]
rs1345103	0.85[CHB][hapmap];0.95[JPT][hapmap]
rs1919708	0.81[ASN][1000 genomes]
rs1919712	0.90[CHB][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs1919713	0.89[JPT][hapmap]
rs2289805	0.90[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap]
rs2440861	0.89[JPT][hapmap]
rs2463959	0.89[JPT][hapmap]
rs2463960	0.84[CHB][hapmap];0.95[JPT][hapmap]
rs2698761	0.89[CHB][hapmap];0.95[JPT][hapmap]
rs2698766	0.89[JPT][hapmap]
rs2698767	0.85[CHB][hapmap];0.95[JPT][hapmap]
rs3827680	0.90[CHB][hapmap];0.95[JPT][hapmap]
rs3950310	0.90[ASN][1000 genomes]
rs4838590	0.90[CHB][hapmap];0.95[JPT][hapmap]
rs61840543	0.91[ASN][1000 genomes]
rs6537560	0.81[ASN][1000 genomes]
rs6537561	0.95[CHB][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs7072515	0.90[CHB][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs7075976	0.95[CHB][hapmap];0.95[JPT][hapmap]
rs7086070	0.83[ASN][1000 genomes]
rs7086275	0.95[CHB][hapmap];0.89[JPT][hapmap]
rs7101060	0.95[CHB][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs734371	0.85[CHB][hapmap];0.95[JPT][hapmap]
rs8428	0.89[CHB][hapmap];0.95[JPT][hapmap]
rs867631	0.81[ASN][1000 genomes]
rs883604	0.81[ASN][1000 genomes]
rs9284	0.90[CHB][hapmap];0.95[JPT][hapmap]
rs9888128	0.89[CHB][hapmap];0.95[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv895366	chr10:49299274-49576454	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	nsv895367	chr10:49333754-49491047	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv895368	chr10:49381635-49551560	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv467190	chr10:49402084-49576878	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	nsv550811	chr10:49402084-49576878	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	nsv550812	chr10:49484698-49524715	Enhancers Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:49466800-49492400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr10:49487600-49488800	Enhancers	GM12878-XiMat	blood

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