Variant report

Variant	rs56842412
Chromosome Location	chr12:45683538-45683539
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	BATF	chr12:45683446-45683686	GM12878	blood:	n/a	n/a
2	TBL1XR1	chr12:45683453-45683718	GM12878	blood:	n/a	n/a
3	SPI1	chr12:45683419-45683721	GM12878	blood:	n/a	n/a
4	BHLHE40	chr12:45683471-45683701	GM12878	blood:	n/a	n/a
5	BCL3	chr12:45683451-45683658	GM12878	blood:	n/a	chr12:45683522-45683531
6	RUNX3	chr12:45683404-45683779	GM12878	blood:	n/a	n/a
7	BCL11A	chr12:45683374-45683724	GM12878	blood:	n/a	chr12:45683522-45683531
8	PAX5	chr12:45683408-45683676	GM12891	blood:	n/a	chr12:45683519-45683528
9	SPI1	chr12:45683288-45683781	GM12878	blood:	n/a	n/a
10	NFIC	chr12:45683350-45683745	GM12878	blood:	n/a	n/a
11	SPI1	chr12:45683363-45683643	GM12891	blood:	n/a	n/a
12	ATF2	chr12:45683407-45683662	GM12878	blood:	n/a	n/a
13	SPI1	chr12:45683376-45683653	GM12891	blood:	n/a	n/a
14	BCL11A	chr12:45683422-45683657	GM12878	blood:	n/a	chr12:45683522-45683531
15	EP300	chr12:45683410-45683733	GM12878	blood:	n/a	chr12:45683517-45683531
16	CUX1	chr12:45683407-45683762	GM12878	blood:	n/a	n/a
17	STAT3	chr12:45683533-45683562	GM12878	blood:	n/a	n/a
18	RUNX3	chr12:45683404-45683683	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:45677743..45680287-chr12:45681430..45684437,3	MCF-7	breast:

Variant related genes	Relation type
ANO6	TF binding region

Extended variants
information (count: 52 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs17095452	0.87[AFR][1000 genomes]
rs55994528	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56162044	1.00[AMR][1000 genomes]
rs56409009	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56672176	0.86[AFR][1000 genomes]
rs57283482	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57514011	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57516582	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57590365	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57752448	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58025806	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58379974	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58615264	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58938625	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58992779	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59111701	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59344692	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59579391	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60098273	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60717004	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61226604	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61679354	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61740396	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74080326	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74080682	0.86[AFR][1000 genomes]
rs74080804	1.00[AMR][1000 genomes]
rs74080853	0.86[AFR][1000 genomes]
rs74080929	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74080930	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74080931	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74080935	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74080976	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74080979	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74080982	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74080983	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74080985	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74080987	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74080989	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74080993	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74080995	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74080997	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74083221	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74083224	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74083303	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74083306	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74083321	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74083322	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74083403	0.82[AFR][1000 genomes]
rs74083404	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74083405	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1050923	chr12:45581310-45808289	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv690	chr12:45674127-45718859	Weak transcription Enhancers Genic enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:45654400-45725600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr12:45662800-45685400	Weak transcription	Primary B cells from peripheral blood	blood
3	chr12:45662800-45696800	Weak transcription	Primary T cells fromperipheralblood	blood
4	chr12:45666200-45709200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
5	chr12:45668400-45697800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
6	chr12:45668600-45693000	Weak transcription	Pancreas	Pancrea
7	chr12:45674200-45706800	Weak transcription	Primary T helper cells fromperipheralblood	blood
8	chr12:45674400-45692200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr12:45674600-45686400	Weak transcription	K562	blood
10	chr12:45675800-45709000	Weak transcription	Lung	lung
11	chr12:45676000-45686600	Weak transcription	Right Atrium	heart
12	chr12:45676200-45693000	Weak transcription	Fetal Stomach	stomach
13	chr12:45676400-45685600	Weak transcription	Primary B cells from cord blood	blood
14	chr12:45676400-45696000	Weak transcription	Fetal Thymus	thymus
15	chr12:45676400-45697800	Weak transcription	Dnd41	blood
16	chr12:45676400-45740400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
17	chr12:45677000-45689800	Weak transcription	Liver	Liver
18	chr12:45677000-45696000	Weak transcription	Primary monocytes fromperipheralblood	blood
19	chr12:45677600-45698200	Weak transcription	Primary T cells from cord blood	blood
20	chr12:45677800-45691800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
21	chr12:45677800-45696000	Weak transcription	Monocytes-CD14+_RO01746	blood
22	chr12:45678400-45684000	Weak transcription	Small Intestine	intestine
23	chr12:45678400-45684200	Weak transcription	Skeletal Muscle Female	skeletal muscle
24	chr12:45678400-45686000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr12:45678400-45688000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr12:45678600-45683600	Weak transcription	Skeletal Muscle Male	skeletal muscle
27	chr12:45678600-45683600	Weak transcription	HSMM	muscle
28	chr12:45678600-45684200	Weak transcription	Fetal Muscle Leg	muscle
29	chr12:45678600-45686400	Weak transcription	Ovary	ovary
30	chr12:45678600-45691800	Weak transcription	HUVEC	blood vessel
31	chr12:45678800-45683600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr12:45678800-45685600	Weak transcription	Adipose Nuclei	Adipose
33	chr12:45678800-45686400	Weak transcription	Fetal Lung	lung
34	chr12:45679200-45683600	Weak transcription	HMEC	breast
35	chr12:45679200-45683600	Weak transcription	Osteobl	bone
36	chr12:45679200-45683800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr12:45679200-45692200	Weak transcription	NHDF-Ad	bronchial
38	chr12:45679400-45683600	Weak transcription	Hela-S3	cervix
39	chr12:45679400-45684200	Weak transcription	NHLF	lung
40	chr12:45679600-45684000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr12:45679800-45684200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr12:45679800-45684600	Weak transcription	Thymus	Thymus
43	chr12:45679800-45685600	Weak transcription	Fetal Heart	heart
44	chr12:45679800-45686400	Weak transcription	Aorta	Aorta
45	chr12:45679800-45686400	Weak transcription	Left Ventricle	heart
46	chr12:45679800-45692200	Weak transcription	NH-A	brain
47	chr12:45680000-45683600	Weak transcription	Placenta Amnion	Placenta Amnion
48	chr12:45680000-45736800	Weak transcription	Fetal Intestine Small	intestine
49	chr12:45680200-45692600	Weak transcription	Fetal Intestine Large	intestine
50	chr12:45680400-45697600	Weak transcription	ES-I3 Cell Line	embryonic stem cell

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