Variant report

Variant	rs513638
Chromosome Location	chr11:120056738-120056739
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	POLR2A	chr11:120054324-120056805	HepG2	liver:	n/a	n/a
2	HEY1	chr11:120055649-120057285	HepG2	liver:	n/a	n/a
3	POLR2A	chr11:120055162-120056941	HepG2	liver:	n/a	n/a
4	EP300	chr11:120056681-120056991	SK-N-SH_RA	brain:	n/a	n/a
5	REST	chr11:120056697-120056980	SK-N-SH	brain:	n/a	n/a
6	MYBL2	chr11:120055621-120056896	HepG2	liver:	n/a	n/a
7	POLR2A	chr11:120055424-120058056	HepG2	liver:	n/a	n/a
8	HEY1	chr11:120055185-120056898	HepG2	liver:	n/a	n/a

Variant related genes	Relation type
TRIM29	TF binding region

Extended variants
information (count: 29 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10790369	0.85[MEX][hapmap]
rs10892546	1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10892547	0.96[ASN][1000 genomes]
rs11217742	0.85[MEX][hapmap]
rs11217749	0.85[MEX][hapmap]
rs12273399	0.96[ASN][1000 genomes]
rs12278345	0.95[ASN][1000 genomes]
rs12419511	0.82[MEX][hapmap]
rs12422179	1.00[MEX][hapmap]
rs2444239	0.96[ASN][1000 genomes]
rs2508491	0.85[EUR][1000 genomes]
rs2508492	1.00[CEU][hapmap];0.80[YRI][hapmap]
rs481599	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs507419	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs508205	0.86[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs508266	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs546441	1.00[CEU][hapmap]
rs547897	0.85[EUR][1000 genomes]
rs548215	1.00[CEU][hapmap]
rs551843	1.00[CEU][hapmap]
rs561218	0.85[EUR][1000 genomes]
rs571854	0.85[EUR][1000 genomes]
rs579368	1.00[CEU][hapmap];1.00[TSI][hapmap]
rs7116997	0.86[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs7118957	0.85[MEX][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:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:120043600-120057000	Weak transcription	Esophagus	oesophagus
2	chr11:120049400-120059800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
3	chr11:120049600-120057000	Weak transcription	Left Ventricle	heart
4	chr11:120051600-120057600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr11:120051800-120057000	Weak transcription	HMEC	breast
6	chr11:120051800-120057200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr11:120052000-120057200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr11:120052000-120057400	Weak transcription	NH-A	brain
9	chr11:120052200-120058200	Weak transcription	Fetal Brain Female	brain
10	chr11:120052600-120058200	Enhancers	Fetal Lung	lung
11	chr11:120053000-120057400	Weak transcription	Brain Angular Gyrus	brain
12	chr11:120053000-120057800	Flanking Active TSS	HepG2	liver
13	chr11:120053800-120058000	Enhancers	NHDF-Ad	bronchial
14	chr11:120054200-120057200	Weak transcription	Brain Cingulate Gyrus	brain
15	chr11:120054200-120057600	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr11:120054400-120057600	Weak transcription	Fetal Heart	heart
17	chr11:120054600-120057000	Weak transcription	Right Atrium	heart
18	chr11:120054600-120057000	Weak transcription	Right Ventricle	heart
19	chr11:120054800-120056800	Weak transcription	Brain Anterior Caudate	brain
20	chr11:120054800-120057800	Enhancers	Fetal Kidney	kidney
21	chr11:120055400-120057400	Enhancers	Placenta	Placenta
22	chr11:120055400-120057600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr11:120055400-120057600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr11:120055400-120058200	Enhancers	Stomach Mucosa	stomach
25	chr11:120055400-120058800	Enhancers	NHLF	lung
26	chr11:120055400-120059400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr11:120055600-120057000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr11:120055600-120057200	Enhancers	Brain Germinal Matrix	brain
29	chr11:120055600-120057200	Weak transcription	Brain Hippocampus Middle	brain
30	chr11:120055600-120058400	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr11:120055600-120059000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr11:120055800-120056800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
33	chr11:120055800-120057000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr11:120055800-120058400	Enhancers	Fetal Brain Male	brain
35	chr11:120055800-120058600	Enhancers	Breast Myoepithelial Primary Cells	Breast
36	chr11:120055800-120059000	Enhancers	Small Intestine	intestine
37	chr11:120055800-120059400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr11:120056000-120056800	Enhancers	HSMMtube	muscle
39	chr11:120056000-120058200	Enhancers	Spleen	Spleen
40	chr11:120056000-120058600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
41	chr11:120056000-120060200	Enhancers	Ovary	ovary
42	chr11:120056000-120064600	Enhancers	Fetal Stomach	stomach
43	chr11:120056200-120057200	Weak transcription	Rectal Smooth Muscle	rectum
44	chr11:120056200-120057800	Enhancers	Adipose Nuclei	Adipose
45	chr11:120056200-120057800	Enhancers	Colonic Mucosa	Colon
46	chr11:120056200-120058000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr11:120056200-120058200	Enhancers	Liver	Liver
48	chr11:120056200-120058200	Enhancers	Fetal Intestine Small	intestine
49	chr11:120056200-120058200	Enhancers	Fetal Muscle Leg	muscle
50	chr11:120056200-120058800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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