Variant report

Variant	rs11112468
Chromosome Location	chr12:105720972-105720973
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	BCLAF1	chr12:105720545-105721286	GM12878	blood:	n/a	n/a
2	JUN	chr12:105720664-105721026	HUVEC	blood vessel:	n/a	chr12:105720864-105720875
3	FOXM1	chr12:105720468-105721131	GM12878	blood:	n/a	n/a
4	FOS	chr12:105720650-105721010	MCF10A-Er-Src	breast:	n/a	chr12:105720864-105720875 chr12:105720861-105720872
5	MYC	chr12:105720739-105720973	MCF10A-Er-Src	breast:	n/a	n/a
6	IKZF1	chr12:105720457-105721780	GM12878	blood:	n/a	n/a
7	TBP	chr12:105720604-105720981	GM12878	blood:	n/a	n/a
8	BHLHE40	chr12:105720705-105721059	GM12878	blood:	n/a	n/a
9	MAZ	chr12:105720657-105721269	GM12878	blood:	n/a	n/a
10	POLR2A	chr12:105720497-105721103	HUVEC	blood vessel:	n/a	n/a
11	E2F4	chr12:105720755-105720996	MCF10A-Er-Src	breast:	n/a	n/a
12	PBX3	chr12:105720464-105721110	SK-N-SH	brain:	n/a	n/a
13	MTA3	chr12:105720427-105721081	GM12878	blood:	n/a	n/a
14	GATA3	chr12:105720453-105721158	SK-N-SH	brain:	n/a	chr12:105720830-105720840
15	NFIC	chr12:105720409-105721840	GM12878	blood:	n/a	n/a
16	BCL11A	chr12:105720616-105721028	GM12878	blood:	n/a	n/a
17	EP300	chr12:105720440-105721169	SK-N-SH	brain:	n/a	n/a
18	EP300	chr12:105720595-105721062	GM12878	blood:	n/a	n/a
19	FOS	chr12:105720557-105721075	HUVEC	blood vessel:	n/a	chr12:105720864-105720875 chr12:105720861-105720872
20	TCF12	chr12:105720437-105721201	SK-N-SH	brain:	n/a	n/a
21	STAT3	chr12:105720651-105721129	GM12878	blood:	n/a	chr12:105720923-105720931 chr12:105720687-105720698 chr12:105720754-105720765
22	TCF3	chr12:105720680-105720999	GM12878	blood:	n/a	n/a
23	NFIC	chr12:105720558-105721196	GM12878	blood:	n/a	n/a
24	EP300	chr12:105720626-105721062	GM12878	blood:	n/a	n/a
25	ZNF384	chr12:105720352-105721408	GM12878	blood:	n/a	n/a
26	MXI1	chr12:105720565-105720993	GM12878	blood:	n/a	n/a
27	BATF	chr12:105720698-105720992	GM12878	blood:	n/a	chr12:105720863-105720874
28	FOSL2	chr12:105720575-105721128	SK-N-SH	brain:	n/a	chr12:105720864-105720875
29	FOS	chr12:105720695-105721010	MCF10A-Er-Src	breast:	n/a	chr12:105720864-105720875 chr12:105720861-105720872
30	SRF	chr12:105720756-105721002	GM12878	blood:	n/a	chr12:105720926-105720939
31	IRF4	chr12:105720658-105721007	GM12878	blood:	n/a	n/a
32	ATF2	chr12:105720581-105721139	GM12878	blood:	n/a	n/a
33	MAX	chr12:105720454-105721002	NB4	blood:	n/a	n/a
34	TBL1XR1	chr12:105720697-105721117	GM12878	blood:	n/a	n/a
35	FOS	chr12:105720651-105721052	MCF10A-Er-Src	breast:	n/a	chr12:105720864-105720875 chr12:105720861-105720872
36	STAT3	chr12:105720711-105720981	MCF10A-Er-Src	breast:	n/a	chr12:105720923-105720931 chr12:105720754-105720765
37	TCF12	chr12:105720484-105721198	SK-N-SH	brain:	n/a	n/a
38	RUNX3	chr12:105720454-105721026	GM12878	blood:	n/a	n/a
39	STAT5A	chr12:105720662-105720977	GM12878	blood:	n/a	chr12:105720923-105720931 chr12:105720687-105720698
40	CHD1	chr12:105720526-105721222	GM12878	blood:	n/a	n/a
41	BATF	chr12:105720666-105720974	GM12878	blood:	n/a	chr12:105720863-105720874
42	RUNX3	chr12:105720301-105721109	GM12878	blood:	n/a	n/a
43	PBX3	chr12:105720521-105721030	SK-N-SH	brain:	n/a	n/a
44	NFATC1	chr12:105720555-105721066	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:105720223..105722150-chr12:105723159..105726102,2	MCF-7	breast:

Variant related genes	Relation type
C12orf75	TF binding region
ENSG00000257642	TF binding region
ENSG00000235162	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10861388	0.80[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10861396	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11112461	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11112465	0.94[CEU][hapmap];1.00[CHB][hapmap];0.92[YRI][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11112467	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11112469	1.00[CHB][hapmap]
rs11112482	1.00[CHB][hapmap]
rs11112499	1.00[CHB][hapmap]
rs11513891	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11519725	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11613789	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12822314	0.94[EUR][1000 genomes]
rs12827086	0.95[EUR][1000 genomes]
rs12828874	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2163718	0.90[ASN][1000 genomes]
rs35407439	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs35561158	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4545651	0.93[CEU][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7303242	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7303307	0.89[YRI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7342398	0.90[ASN][1000 genomes]
rs7959385	0.94[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7972400	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7972676	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7972982	0.82[AMR][1000 genomes];0.98[EUR][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	nsv899499	chr12:105616297-105722529	Bivalent Enhancer Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
2	nsv510589	chr12:105670071-105743755	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:105713400-105724000	Weak transcription	Pancreas	Pancrea
2	chr12:105713800-105723800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
3	chr12:105714600-105724000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr12:105715800-105723800	Weak transcription	Primary hematopoietic stem cells	blood
5	chr12:105716000-105723800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr12:105716400-105723800	Weak transcription	HSMMtube	muscle
7	chr12:105716600-105723600	Weak transcription	Skeletal Muscle Female	skeletal muscle
8	chr12:105716600-105723800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr12:105716800-105723600	Weak transcription	Skeletal Muscle Male	skeletal muscle
10	chr12:105716800-105723800	Weak transcription	Fetal Intestine Large	intestine
11	chr12:105718000-105723800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
12	chr12:105718200-105721000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
13	chr12:105718200-105723800	Weak transcription	Stomach Mucosa	stomach
14	chr12:105719000-105723800	Weak transcription	Fetal Intestine Small	intestine
15	chr12:105719000-105723800	Weak transcription	HSMM	muscle
16	chr12:105719000-105724000	Weak transcription	Thymus	Thymus
17	chr12:105719600-105721200	Enhancers	HMEC	breast
18	chr12:105719800-105721400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr12:105719800-105721400	Enhancers	Dnd41	blood
20	chr12:105719800-105721400	Enhancers	NH-A	brain
21	chr12:105720000-105721200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr12:105720000-105721200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr12:105720000-105721800	Enhancers	Primary T cells fromperipheralblood	blood
24	chr12:105720000-105723800	Enhancers	Primary hematopoietic stem cells short term culture	blood
25	chr12:105720200-105721200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr12:105720400-105721200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr12:105720400-105721200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr12:105720400-105721200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr12:105720400-105721200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr12:105720400-105721200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
31	chr12:105720400-105721200	Enhancers	A549	lung
32	chr12:105720400-105721200	Flanking Active TSS	HUVEC	blood vessel
33	chr12:105720400-105721200	Enhancers	NHEK	skin
34	chr12:105720400-105721200	Enhancers	NHLF	lung
35	chr12:105720400-105721400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr12:105720400-105721400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr12:105720400-105721400	Flanking Active TSS	GM12878-XiMat	blood
38	chr12:105720400-105721800	Enhancers	Primary B cells from peripheral blood	blood
39	chr12:105720400-105723800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr12:105720600-105721000	Enhancers	Pancreatic Islets	Pancreatic Islet
41	chr12:105720600-105721000	Weak transcription	Rectal Mucosa Donor 31	rectum
42	chr12:105720600-105721000	Active TSS	NHDF-Ad	bronchial
43	chr12:105720600-105721200	Enhancers	Primary T helper naive cells from peripheral blood	blood
44	chr12:105720600-105721200	Enhancers	Osteobl	bone
45	chr12:105720800-105721000	Enhancers	Primary B cells from cord blood	blood
46	chr12:105720800-105721000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
47	chr12:105720800-105721000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr12:105720800-105721000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr12:105720800-105721200	Enhancers	Hela-S3	cervix
50	chr12:105720800-105722400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood

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