Variant report

Variant	rs12422179
Chromosome Location	chr11:120057729-120057730
allele	G/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	WRNIP1	chr11:120057562-120057743	GM12878	blood:	n/a	n/a
2	FOS	chr11:120057589-120057902	MCF10A-Er-Src	breast:	n/a	n/a
3	MYC	chr11:120057491-120057857	MCF10A-Er-Src	breast:	n/a	n/a
4	EP300	chr11:120057577-120057998	GM12878	blood:	n/a	chr11:120057663-120057672
5	NFIC	chr11:120057465-120057811	GM12878	blood:	n/a	n/a
6	BATF	chr11:120057514-120058006	GM12878	blood:	n/a	n/a
7	EBF1	chr11:120057373-120058044	GM12878	blood:	n/a	chr11:120057627-120057637 chr11:120057627-120057636 chr11:120057626-120057637
8	PAX5	chr11:120057699-120057982	GM12878	blood:	n/a	n/a
9	FOS	chr11:120057640-120057882	MCF10A-Er-Src	breast:	n/a	n/a
10	TCF12	chr11:120057485-120057796	GM12878	blood:	n/a	n/a
11	EP300	chr11:120057528-120057970	GM12878	blood:	n/a	chr11:120057663-120057672
12	EBF1	chr11:120057089-120058070	GM12878	blood:	n/a	chr11:120057627-120057637 chr11:120057627-120057636 chr11:120057626-120057637
13	MTA3	chr11:120057376-120058005	GM12878	blood:	n/a	n/a
14	PAX5	chr11:120057558-120058080	GM12878	blood:	n/a	n/a
15	STAT3	chr11:120057707-120057741	MCF10A-Er-Src	breast:	n/a	n/a
16	CHD2	chr11:120057562-120057932	GM12878	blood:	n/a	n/a
17	EBF1	chr11:120057398-120058017	GM12878	blood:	n/a	chr11:120057627-120057637 chr11:120057627-120057636 chr11:120057626-120057637
18	IRF4	chr11:120057636-120058038	GM12878	blood:	n/a	n/a
19	ZNF143	chr11:120057510-120057798	GM12878	blood:	n/a	n/a
20	ATF2	chr11:120057426-120057861	GM12878	blood:	n/a	n/a
21	RFX5	chr11:120057643-120057926	HepG2	liver:	n/a	n/a
22	RCOR1	chr11:120057552-120057744	HepG2	liver:	n/a	n/a
23	MAFK	chr11:120057563-120057939	IMR90	lung:	n/a	chr11:120057750-120057766 chr11:120057751-120057765 chr11:120057752-120057761 chr11:120057748-120057768
24	MAFK	chr11:120057530-120057954	HepG2	liver:	n/a	chr11:120057750-120057766 chr11:120057751-120057765 chr11:120057752-120057761 chr11:120057748-120057768
25	USF2	chr11:120057644-120058114	GM12878	blood:	n/a	n/a
26	TBP	chr11:120057726-120058172	HepG2	liver:	n/a	n/a
27	FOS	chr11:120057538-120057922	MCF10A-Er-Src	breast:	n/a	n/a
28	SP1	chr11:120057481-120057820	GM12878	blood:	n/a	n/a
29	PAX5	chr11:120057456-120058130	GM12878	blood:	n/a	n/a
30	MAFK	chr11:120057584-120058128	HepG2	liver:	n/a	chr11:120057750-120057766 chr11:120057751-120057765 chr11:120057752-120057761 chr11:120057748-120057768
31	RUNX3	chr11:120057460-120057892	GM12878	blood:	n/a	n/a
32	PAX5	chr11:120057531-120058053	GM12878	blood:	n/a	n/a
33	RELA	chr11:120057367-120058001	GM18951	blood:	n/a	n/a
34	RXRA	chr11:120057376-120057785	HepG2	liver:	n/a	chr11:120057561-120057577
35	FOS	chr11:120057586-120057823	MCF10A-Er-Src	breast:	n/a	n/a
36	STAT3	chr11:120057600-120057800	MCF10A-Er-Src	breast:	n/a	n/a
37	CUX1	chr11:120057565-120057841	GM12878	blood:	n/a	n/a
38	RELA	chr11:120057485-120058010	GM19099	blood:	n/a	n/a
39	RUNX3	chr11:120057458-120057964	GM12878	blood:	n/a	n/a
40	MAX	chr11:120057461-120058078	GM12878	blood:	n/a	chr11:120057927-120057940 chr11:120057928-120057939 chr11:120057924-120057943 chr11:120057929-120057938
41	POLR2A	chr11:120055424-120058056	HepG2	liver:	n/a	n/a
42	MAFF	chr11:120057575-120058282	HepG2	liver:	n/a	chr11:120057751-120057765 chr11:120057752-120057770
43	MAX	chr11:120057487-120058168	HepG2	liver:	n/a	chr11:120057927-120057940 chr11:120057928-120057939 chr11:120057924-120057943 chr11:120057929-120057938
44	TBL1XR1	chr11:120057486-120058147	GM12878	blood:	n/a	n/a
45	BHLHE40	chr11:120057486-120058102	GM12878	blood:	n/a	n/a
46	EP300	chr11:120057479-120058010	GM12878	blood:	n/a	chr11:120057663-120057672

Variant related genes	Relation type
TRIM29	TF binding region

Extended variants
information (count: 88 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:84)

rs_ID	r²[population]
rs10790369	1.00[GIH][hapmap];0.81[JPT][hapmap];0.85[MEX][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10892544	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10892545	0.89[AMR][1000 genomes]
rs10892546	1.00[MEX][hapmap]
rs11217699	0.85[GIH][hapmap]
rs11217701	0.84[AMR][1000 genomes]
rs11217702	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11217705	0.83[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11217706	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11217707	0.94[AMR][1000 genomes]
rs11217708	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11217710	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11217711	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11217713	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11217715	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11217716	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11217718	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11217719	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11217720	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11217721	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11217722	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11217723	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11217724	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11217725	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11217726	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11217727	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11217728	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11217729	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11217730	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11217731	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11217732	0.82[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11217733	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11217734	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11217735	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11217736	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11217737	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11217738	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11217739	0.83[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11217740	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11217741	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11217742	1.00[GIH][hapmap];0.83[JPT][hapmap];0.85[MEX][hapmap];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11217743	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11217744	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11217745	0.89[AMR][1000 genomes]
rs11217746	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11217748	0.83[JPT][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11217749	1.00[GIH][hapmap];0.83[JPT][hapmap];0.85[MEX][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11217750	0.81[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11217751	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11217753	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11217754	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11535714	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12049837	0.81[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12224041	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12224472	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12225418	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12274981	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12281157	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12283165	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12291620	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs12417084	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12417094	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12417234	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12418352	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12419511	1.00[GIH][hapmap];0.83[JPT][hapmap];0.82[MEX][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12419830	0.84[AMR][1000 genomes]
rs12419976	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12419985	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12420591	0.93[ASN][1000 genomes]
rs12420985	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12421218	0.94[AMR][1000 genomes]
rs34981150	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3740728	0.83[JPT][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3740729	0.83[JPT][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3740730	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3740731	0.83[JPT][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs508266	1.00[MEX][hapmap]
rs513638	1.00[MEX][hapmap]
rs679074	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7118957	1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7119349	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7119458	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs880487	0.88[ASN][1000 genomes]
rs896693	1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1054057	chr11:119781953-120519770	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv541178	chr11:119781953-120519770	Weak transcription Enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	nsv428581	chr11:120006048-120167603	Strong transcription Active TSS Bivalent Enhancer Enhancers Flanking Active TSS Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
4	nsv518464	chr11:120040442-120109967	Genic enhancers Enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:70 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:120049400-120059800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
2	chr11:120052200-120058200	Weak transcription	Fetal Brain Female	brain
3	chr11:120052600-120058200	Enhancers	Fetal Lung	lung
4	chr11:120053000-120057800	Flanking Active TSS	HepG2	liver
5	chr11:120053800-120058000	Enhancers	NHDF-Ad	bronchial
6	chr11:120054800-120057800	Enhancers	Fetal Kidney	kidney
7	chr11:120055400-120058200	Enhancers	Stomach Mucosa	stomach
8	chr11:120055400-120058800	Enhancers	NHLF	lung
9	chr11:120055400-120059400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr11:120055600-120058400	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr11:120055600-120059000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr11:120055800-120058400	Enhancers	Fetal Brain Male	brain
13	chr11:120055800-120058600	Enhancers	Breast Myoepithelial Primary Cells	Breast
14	chr11:120055800-120059000	Enhancers	Small Intestine	intestine
15	chr11:120055800-120059400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr11:120056000-120058200	Enhancers	Spleen	Spleen
17	chr11:120056000-120058600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
18	chr11:120056000-120060200	Enhancers	Ovary	ovary
19	chr11:120056000-120064600	Enhancers	Fetal Stomach	stomach
20	chr11:120056200-120057800	Enhancers	Adipose Nuclei	Adipose
21	chr11:120056200-120057800	Enhancers	Colonic Mucosa	Colon
22	chr11:120056200-120058000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr11:120056200-120058200	Enhancers	Liver	Liver
24	chr11:120056200-120058200	Enhancers	Fetal Intestine Small	intestine
25	chr11:120056200-120058200	Enhancers	Fetal Muscle Leg	muscle
26	chr11:120056200-120058800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr11:120056200-120059200	Enhancers	Fetal Intestine Large	intestine
28	chr11:120056200-120060800	Enhancers	Pancreas	Pancrea
29	chr11:120056400-120058200	Enhancers	Fetal Muscle Trunk	muscle
30	chr11:120056400-120059000	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
31	chr11:120056400-120060200	Enhancers	Sigmoid Colon	Sigmoid Colon
32	chr11:120056600-120057800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr11:120056600-120058000	Weak transcription	Cortex derived primary cultured neurospheres	brain
34	chr11:120056600-120058200	Enhancers	Colon Smooth Muscle	Colon
35	chr11:120056600-120058200	Enhancers	Duodenum Smooth Muscle	Duodenum
36	chr11:120056800-120057800	Weak transcription	HSMMtube	muscle
37	chr11:120056800-120058600	Enhancers	Brain Anterior Caudate	brain
38	chr11:120056800-120059600	Enhancers	Duodenum Mucosa	Duodenum
39	chr11:120057000-120057800	Enhancers	Stomach Smooth Muscle	stomach
40	chr11:120057000-120057800	Enhancers	HMEC	breast
41	chr11:120057000-120058000	Enhancers	Left Ventricle	heart
42	chr11:120057000-120058000	Enhancers	Right Atrium	heart
43	chr11:120057000-120058200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr11:120057000-120058200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr11:120057000-120058200	Enhancers	Right Ventricle	heart
46	chr11:120057000-120058400	Enhancers	GM12878-XiMat	blood
47	chr11:120057000-120058600	Enhancers	Esophagus	oesophagus
48	chr11:120057000-120059400	Enhancers	Skeletal Muscle Female	skeletal muscle
49	chr11:120057200-120058000	Enhancers	Lung	lung
50	chr11:120057200-120058000	Enhancers	NHEK	skin

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