Variant report

Variant	rs72804451
Chromosome Location	chr2:47041235-47041236
allele	C/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	NFIC	chr2:47041128-47041884	SK-N-SH	brain:	n/a	n/a
2	EP300	chr2:47037776-47041932	SK-N-SH	brain:	n/a	chr2:47041533-47041547 chr2:47038862-47038876 chr2:47039929-47039943
3	PBX3	chr2:47041114-47041817	SK-N-SH	brain:	n/a	chr2:47041455-47041475

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:47040061..47042804-chr2:47072959..47074539,2	MCF-7	breast:

Variant related genes	Relation type
LINC01118	TF binding region
LINC01119	TF binding region
ENSG00000239332	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs17035709	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17824594	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55980660	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs56060227	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs56172110	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72804436	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs72804437	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs72804438	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs72804445	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72804446	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72804450	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72804452	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72804458	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72804469	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs72804470	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]

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:65 , 50 per page) page: 1 2

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	chr2:47037600-47042400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr2:47038000-47042600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr2:47038200-47042400	Enhancers	Fetal Stomach	stomach
6	chr2:47038200-47042600	Enhancers	NHDF-Ad	bronchial
7	chr2:47038200-47042800	Enhancers	Colon Smooth Muscle	Colon
8	chr2:47038400-47041400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr2:47038400-47041600	Enhancers	Fetal Lung	lung
10	chr2:47038600-47042000	Enhancers	Brain Anterior Caudate	brain
11	chr2:47038600-47042000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
12	chr2:47038600-47042400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr2:47038600-47042400	Enhancers	Fetal Muscle Leg	muscle
14	chr2:47038600-47042400	Enhancers	Ovary	ovary
15	chr2:47038600-47042400	Enhancers	Skeletal Muscle Male	skeletal muscle
16	chr2:47038600-47042600	Enhancers	Rectal Smooth Muscle	rectum
17	chr2:47038600-47042600	Enhancers	Skeletal Muscle Female	skeletal muscle
18	chr2:47038600-47042800	Enhancers	Left Ventricle	heart
19	chr2:47038600-47046400	Enhancers	Lung	lung
20	chr2:47038600-47046400	Enhancers	Right Atrium	heart
21	chr2:47038800-47041800	Enhancers	Fetal Muscle Trunk	muscle
22	chr2:47038800-47042800	Enhancers	Fetal Heart	heart
23	chr2:47038800-47043800	Enhancers	Placenta	Placenta
24	chr2:47038800-47044000	Weak transcription	Esophagus	oesophagus
25	chr2:47038800-47046200	Enhancers	Right Ventricle	heart
26	chr2:47039200-47042000	Enhancers	Colonic Mucosa	Colon
27	chr2:47039200-47042200	Enhancers	Adipose Nuclei	Adipose
28	chr2:47039600-47041600	Enhancers	Muscle Satellite Cultured Cells	--
29	chr2:47039600-47041600	Weak transcription	Psoas Muscle	Psoas
30	chr2:47039600-47041800	Enhancers	Aorta	Aorta
31	chr2:47039800-47041600	Weak transcription	Fetal Kidney	kidney
32	chr2:47039800-47042000	Enhancers	NHLF	lung
33	chr2:47039800-47042400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr2:47039800-47042400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
35	chr2:47039800-47042800	Enhancers	Breast Myoepithelial Primary Cells	Breast
36	chr2:47039800-47053800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
37	chr2:47040000-47041400	Enhancers	Brain Cingulate Gyrus	brain
38	chr2:47040000-47041800	Enhancers	NH-A	brain
39	chr2:47040000-47042000	Enhancers	Fetal Thymus	thymus
40	chr2:47040200-47041600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr2:47040200-47042000	Weak transcription	Fetal Intestine Small	intestine
42	chr2:47040200-47042200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr2:47040200-47042200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr2:47040200-47044200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr2:47040400-47041600	Weak transcription	Rectal Mucosa Donor 31	rectum
46	chr2:47040400-47042200	Enhancers	Osteobl	bone
47	chr2:47040400-47042600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr2:47040400-47045800	Weak transcription	HMEC	breast
49	chr2:47040600-47041400	Active TSS	Fetal Brain Male	brain
50	chr2:47040600-47041600	Weak transcription	Duodenum Mucosa	Duodenum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links