Variant report

Variant	rs4953425
Chromosome Location	chr2:47042873-47042874
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	RAD21	chr2:47042143-47042880	HCT-116	colon:	n/a	n/a

Variant related genes	Relation type
LINC01119	TF binding region
LINC01118	TF binding region

Extended variants
information (count: 12 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs1053952	0.81[JPT][hapmap];0.85[EUR][1000 genomes]
rs1374273	0.83[CEU][hapmap];0.86[CHB][hapmap];0.88[JPT][hapmap];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1530547	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2289931	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6733709	0.85[EUR][1000 genomes]
rs7590016	0.85[EUR][1000 genomes]
rs7590022	0.85[EUR][1000 genomes]
rs935375	0.94[YRI][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	nsv873996	chr2:46670941-47065227	Strong transcription Enhancers Weak transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv817517	chr2:46819371-47715140	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
3	nsv457352	chr2:47004788-47325973	Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
4	nsv581749	chr2:47004788-47325973	Flanking Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:47031400-47043600	Weak transcription	Spleen	Spleen
2	chr2:47031400-47052000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr2:47038600-47046400	Enhancers	Lung	lung
4	chr2:47038600-47046400	Enhancers	Right Atrium	heart
5	chr2:47038800-47043800	Enhancers	Placenta	Placenta
6	chr2:47038800-47044000	Weak transcription	Esophagus	oesophagus
7	chr2:47038800-47046200	Enhancers	Right Ventricle	heart
8	chr2:47039800-47053800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr2:47040200-47044200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr2:47040400-47045800	Weak transcription	HMEC	breast
11	chr2:47040600-47044800	Weak transcription	Brain Hippocampus Middle	brain
12	chr2:47040600-47045000	Weak transcription	Brain Inferior Temporal Lobe	brain
13	chr2:47040600-47045200	Weak transcription	Cortex derived primary cultured neurospheres	brain
14	chr2:47040600-47045200	Weak transcription	HSMMtube	muscle
15	chr2:47041400-47044200	Weak transcription	Brain Cingulate Gyrus	brain
16	chr2:47041800-47043800	Enhancers	Stomach Smooth Muscle	stomach
17	chr2:47041800-47044000	Weak transcription	Aorta	Aorta
18	chr2:47042000-47044000	Weak transcription	Brain Anterior Caudate	brain
19	chr2:47042000-47044600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr2:47042200-47044200	Weak transcription	Adipose Nuclei	Adipose
21	chr2:47042200-47045000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr2:47042400-47043400	Weak transcription	Skeletal Muscle Male	skeletal muscle
23	chr2:47042400-47044000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr2:47042400-47044400	Weak transcription	Duodenum Smooth Muscle	Duodenum
25	chr2:47042400-47044600	Weak transcription	Ovary	ovary
26	chr2:47042400-47044600	Weak transcription	Rectal Mucosa Donor 31	rectum
27	chr2:47042400-47045000	Weak transcription	Fetal Muscle Leg	muscle
28	chr2:47042400-47047000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr2:47042400-47048800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr2:47042600-47043800	Weak transcription	Skeletal Muscle Female	skeletal muscle
31	chr2:47042600-47044000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr2:47042600-47044000	Weak transcription	Psoas Muscle	Psoas
33	chr2:47042600-47044600	Weak transcription	Rectal Smooth Muscle	rectum
34	chr2:47042600-47045000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr2:47042600-47045000	Weak transcription	NHDF-Ad	bronchial
36	chr2:47042800-47043800	Weak transcription	Fetal Heart	heart
37	chr2:47042800-47043800	Weak transcription	Left Ventricle	heart
38	chr2:47042800-47044000	Weak transcription	Colon Smooth Muscle	Colon
39	chr2:47042800-47044400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr2:47042800-47044600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
41	chr2:47042800-47053400	Weak transcription	Fetal Lung	lung

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