Variant report

Variant	rs56212015
Chromosome Location	chr1:247375362-247375363
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	EP300	chr1:247375211-247375776	GM12878	blood:	n/a	chr1:247375331-247375345
2	ATF2	chr1:247375299-247375715	GM12878	blood:	n/a	n/a
3	ATF2	chr1:247375145-247375751	GM12878	blood:	n/a	n/a
4	EBF1	chr1:247375211-247375849	GM12878	blood:	n/a	n/a
5	CUX1	chr1:247375133-247376192	GM12878	blood:	n/a	n/a
6	EP300	chr1:247375146-247375888	GM12878	blood:	n/a	chr1:247375331-247375345
7	RCOR1	chr1:247375175-247375788	GM12878	blood:	n/a	n/a
8	TAL1	chr1:247375361-247375841	K562	blood:	n/a	n/a
9	BHLHE40	chr1:247375169-247375758	GM12878	blood:	n/a	n/a
10	STAT3	chr1:247375193-247375691	GM12878	blood:	n/a	n/a
11	MXI1	chr1:247375037-247375814	GM12878	blood:	n/a	n/a
12	POU2F2	chr1:247375263-247375673	GM12891	blood:	n/a	chr1:247375323-247375334
13	BCL11A	chr1:247375295-247375710	GM12878	blood:	n/a	n/a
14	TCF3	chr1:247375355-247375781	GM12878	blood:	n/a	n/a
15	TCF12	chr1:247375343-247375729	GM12878	blood:	n/a	n/a
16	BHLHE40	chr1:247375207-247375594	K562	blood:	n/a	n/a
17	NFIC	chr1:247375020-247375764	GM12878	blood:	n/a	chr1:247375251-247375279
18	STAT5A	chr1:247375224-247375709	GM12878	blood:	n/a	n/a
19	PAX5	chr1:247375232-247375674	GM12878	blood:	n/a	chr1:247375440-247375459
20	EP300	chr1:247375350-247375725	GM12878	blood:	n/a	n/a
21	PAX5	chr1:247375292-247375657	GM12878	blood:	n/a	chr1:247375440-247375459
22	PAX5	chr1:247375269-247375682	GM12878	blood:	n/a	chr1:247375440-247375459
23	BATF	chr1:247375294-247375713	GM12878	blood:	n/a	n/a
24	RELA	chr1:247375281-247375760	GM19099	blood:	n/a	n/a
25	RUNX3	chr1:247375187-247375801	GM12878	blood:	n/a	n/a
26	MAFK	chr1:247375335-247375673	HepG2	liver:	n/a	chr1:247375490-247375505
27	PAX5	chr1:247375345-247375605	GM12892	blood:	n/a	chr1:247375440-247375459
28	SIN3A	chr1:247375348-247375768	GM12878	blood:	n/a	n/a
29	MTA3	chr1:247375168-247375706	GM12878	blood:	n/a	n/a
30	ZNF143	chr1:247375289-247375748	GM12878	blood:	n/a	n/a
31	STAT1	chr1:247375179-247375663	GM12878	blood:	n/a	n/a
32	RFX5	chr1:247375334-247375753	GM12878	blood:	n/a	n/a
33	CHD2	chr1:247374928-247375920	GM12878	blood:	n/a	n/a
34	PAX5	chr1:247375177-247375807	GM12878	blood:	n/a	chr1:247375440-247375459
35	TRIM28	chr1:247375282-247375831	K562	blood:	n/a	n/a
36	MTA3	chr1:247375202-247375830	GM12878	blood:	n/a	n/a
37	MAFK	chr1:247375316-247375643	HepG2	liver:	n/a	chr1:247375490-247375505
38	SP1	chr1:247375211-247375756	GM12878	blood:	n/a	n/a
39	TBL1XR1	chr1:247375250-247375970	GM12878	blood:	n/a	n/a
40	FOXM1	chr1:247375171-247375738	GM12878	blood:	n/a	n/a
41	MAFK	chr1:247375250-247375673	K562	blood:	n/a	chr1:247375490-247375505
42	BCLAF1	chr1:247375254-247375784	GM12878	blood:	n/a	n/a
43	STAT5A	chr1:247375277-247375598	GM12878	blood:	n/a	n/a
44	RCOR1	chr1:247375131-247375724	K562	blood:	n/a	n/a
45	MAFF	chr1:247375339-247375679	K562	blood:	n/a	chr1:247375489-247375507
46	PML	chr1:247375177-247375761	GM12878	blood:	n/a	n/a
47	NFYB	chr1:247375103-247375397	GM12878	blood:	n/a	n/a
48	RUNX3	chr1:247375221-247375768	GM12878	blood:	n/a	n/a
49	TCF12	chr1:247375291-247375748	GM12878	blood:	n/a	n/a
50	IRF4	chr1:247375273-247375763	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:247366973..247371599-chr1:247371697..247375755,6	MCF-7	breast:
2	chr1:247374235..247377046-chr1:247498080..247500631,2	K562	blood:
3	chr1:247274493..247276812-chr1:247371838..247375899,3	K562	blood:
4	chr1:247371861..247375582-chr1:247493463..247496360,5	MCF-7	breast:

Variant related genes	Relation type
MIR3916	TF binding region
ENSG00000252516	Chromatin interaction
ENSG00000162714	Chromatin interaction
ENSG00000221953	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs12083552	0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17720872	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs41305576	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55932854	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56036028	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56123640	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs56130102	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56358623	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61087736	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72770359	0.89[AMR][1000 genomes]
rs72770361	0.89[AMR][1000 genomes]
rs72770366	0.93[EUR][1000 genomes]
rs72770367	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs72770371	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs72770374	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs72770379	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72770384	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72770390	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72770391	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1005208	chr1:247037441-247597975	Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Strong transcription Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
2	nsv535417	chr1:247094131-247409000	ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	47 gene(s)	inside rSNPs	diseases
3	nsv1005639	chr1:247094161-247401380	ZNF genes & repeats Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	47 gene(s)	inside rSNPs	diseases
4	nsv535418	chr1:247094161-247401380	Active TSS ZNF genes & repeats Flanking Active TSS Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	47 gene(s)	inside rSNPs	diseases
5	nsv916236	chr1:247124353-247409065	Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Enhancers Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	36 gene(s)	inside rSNPs	diseases
6	nsv948419	chr1:247130577-247400404	ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	35 gene(s)	inside rSNPs	diseases
7	nsv1002438	chr1:247173851-247401380	ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Active TSS Weak transcription Strong transcription Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	30 gene(s)	inside rSNPs	diseases
8	nsv833126	chr1:247273084-247476150	Enhancers ZNF genes & repeats Weak transcription Bivalent Enhancer Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	n/a
9	nsv873436	chr1:247339064-247385877	Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:247373400-247375600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr1:247374200-247379600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr1:247374400-247375400	Weak transcription	HSMM	muscle
4	chr1:247374400-247375600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr1:247374600-247375400	Enhancers	Primary B cells from cord blood	blood
6	chr1:247374600-247375400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr1:247374600-247375600	Enhancers	Esophagus	oesophagus
8	chr1:247374600-247375600	Enhancers	Fetal Intestine Small	intestine
9	chr1:247374600-247376200	Enhancers	Primary B cells from peripheral blood	blood
10	chr1:247374600-247376200	Flanking Active TSS	GM12878-XiMat	blood
11	chr1:247374600-247376800	Enhancers	Primary T helper cells fromperipheralblood	blood
12	chr1:247374600-247376800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
13	chr1:247374600-247377200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
14	chr1:247374600-247377200	Enhancers	Primary T helper naive cells from peripheral blood	blood
15	chr1:247374600-247377200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
16	chr1:247374600-247379600	Weak transcription	Fetal Thymus	thymus
17	chr1:247374800-247375400	Enhancers	ES-I3 Cell Line	embryonic stem cell
18	chr1:247374800-247375600	Enhancers	NHDF-Ad	bronchial
19	chr1:247374800-247377000	Enhancers	Primary T killer memory cells from peripheral blood	blood
20	chr1:247375000-247375600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr1:247375000-247375800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
22	chr1:247375000-247376000	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
23	chr1:247375000-247376400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
24	chr1:247375000-247377200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
25	chr1:247375200-247375400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr1:247375200-247375400	Enhancers	Stomach Mucosa	stomach
27	chr1:247375200-247375400	Enhancers	K562	blood
28	chr1:247375200-247375600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
29	chr1:247375200-247376600	Enhancers	HepG2	liver

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