Variant report

Variant	rs9942353
Chromosome Location	chr5:9055556-9055557
allele	A/C
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	GATA3	chr5:9055169-9055867	SK-N-SH	brain:	n/a	n/a
2	CEBPB	chr5:9055535-9055694	HepG2	liver:	n/a	chr5:9055646-9055657
3	PBX3	chr5:9055295-9055804	SK-N-SH	brain:	n/a	n/a
4	GATA3	chr5:9055159-9055786	SK-N-SH	brain:	n/a	n/a
5	CEBPB	chr5:9055491-9055783	IMR90	lung:	n/a	chr5:9055646-9055657

Variant related genes	Relation type
MIR4636	TF binding region

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs2962652	1.00[AMR][1000 genomes]
rs2962653	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2962725	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2962728	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2962732	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2962736	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2963323	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2963338	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2963346	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2963355	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2963356	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2963361	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2963362	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2963364	1.00[AMR][1000 genomes]
rs2963369	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2963372	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2963373	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2963374	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2963377	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2963381	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2963385	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2963386	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2963387	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2963388	0.94[AFR][1000 genomes];1.00[AMR][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	nsv881438	chr5:8728874-9695667	Enhancers Genic enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	21 gene(s)	inside rSNPs	diseases
2	nsv461944	chr5:8758041-9209831	Weak transcription Enhancers ZNF genes & repeats Genic enhancers Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
3	nsv597069	chr5:8758041-9209831	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
4	nsv1016937	chr5:8824417-9402871	Enhancers Weak transcription Strong transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases
5	nsv537638	chr5:8824417-9402871	Genic enhancers Weak transcription Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases
6	nsv918004	chr5:8824417-9402871	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases
7	nsv482764	chr5:8906261-9056262	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	2 gene(s)	inside rSNPs	diseases
8	nsv1015378	chr5:9053542-9617963	Genic enhancers Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases
9	nsv537640	chr5:9053542-9617963	Bivalent/Poised TSS Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Strong transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:9036600-9057000	Weak transcription	Brain Substantia Nigra	brain
2	chr5:9038400-9056200	Weak transcription	Fetal Kidney	kidney
3	chr5:9038400-9057600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr5:9038800-9063600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
5	chr5:9040200-9064600	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr5:9040800-9122000	Weak transcription	Colonic Mucosa	Colon
7	chr5:9042200-9066600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr5:9042600-9057000	Weak transcription	Brain Cingulate Gyrus	brain
9	chr5:9042800-9057400	Weak transcription	Brain Angular Gyrus	brain
10	chr5:9042800-9057400	Weak transcription	Brain Anterior Caudate	brain
11	chr5:9043200-9057000	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr5:9044800-9057600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr5:9044800-9061400	Weak transcription	Aorta	Aorta
14	chr5:9044800-9065200	Weak transcription	Pancreas	Pancrea
15	chr5:9046600-9065400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr5:9047800-9056200	Weak transcription	Brain Germinal Matrix	brain
17	chr5:9050000-9065200	Weak transcription	Right Ventricle	heart
18	chr5:9051000-9058600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr5:9051000-9065200	Weak transcription	Left Ventricle	heart
20	chr5:9051200-9057600	Weak transcription	Fetal Intestine Small	intestine
21	chr5:9051800-9065200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr5:9052800-9058200	Weak transcription	Fetal Intestine Large	intestine
23	chr5:9053200-9067400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
24	chr5:9053400-9060000	Weak transcription	Ovary	ovary
25	chr5:9053800-9057800	Weak transcription	Duodenum Mucosa	Duodenum
26	chr5:9053800-9077800	Weak transcription	Fetal Heart	heart
27	chr5:9054000-9056400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr5:9054000-9060200	Weak transcription	Liver	Liver
29	chr5:9054000-9061200	Weak transcription	Fetal Muscle Trunk	muscle
30	chr5:9054200-9055600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr5:9054200-9055800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr5:9054200-9056200	Weak transcription	Sigmoid Colon	Sigmoid Colon
33	chr5:9054200-9056400	Enhancers	HMEC	breast
34	chr5:9054200-9056600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr5:9054400-9056200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr5:9054400-9058800	Weak transcription	Fetal Muscle Leg	muscle
37	chr5:9054400-9060400	Weak transcription	Placenta Amnion	Placenta Amnion
38	chr5:9054400-9060600	Weak transcription	Cortex derived primary cultured neurospheres	brain
39	chr5:9054400-9062600	Weak transcription	Rectal Mucosa Donor 31	rectum
40	chr5:9054600-9056600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr5:9054600-9061800	Weak transcription	Rectal Mucosa Donor 29	rectum
42	chr5:9054600-9062600	Weak transcription	Esophagus	oesophagus
43	chr5:9054800-9056000	Enhancers	Breast Myoepithelial Primary Cells	Breast
44	chr5:9055000-9056200	Enhancers	Muscle Satellite Cultured Cells	--
45	chr5:9055000-9056200	Enhancers	Fetal Lung	lung
46	chr5:9055000-9056400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr5:9055000-9056400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr5:9055000-9056400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr5:9055000-9056400	Enhancers	NH-A	brain
50	chr5:9055000-9056400	Enhancers	Osteobl	bone

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