Variant report

Variant	rs58800297
Chromosome Location	chr4:147251566-147251567
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:147165861..147167805-chr4:147250509..147253792,3	MCF-7	breast:
2	chr4:146858016..146860024-chr4:147250231..147252357,2	MCF-7	breast:
3	chr4:147250783..147254830-chr4:147255041..147259510,7	MCF-7	breast:
4	chr4:147096365..147098280-chr4:147250608..147253432,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000151612	Chromatin interaction
ENSG00000164167	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10519784	0.96[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs10519786	0.96[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs10519805	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs16998677	0.96[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs17021340	0.96[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs17021345	0.96[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs17021355	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17021362	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17021365	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17021409	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2291379	0.96[AMR][1000 genomes]
rs4561947	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs57305184	0.96[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs58203372	1.00[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs58738547	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs58997046	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs59524631	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs59758996	0.96[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs59811977	0.96[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs59890707	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59916828	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs59937090	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs60175042	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs60862748	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61016468	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61219941	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv461675	chr4:147116864-147768206	Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
2	nsv595651	chr4:147116864-147768206	Weak transcription Enhancers Genic enhancers Bivalent/Poised TSS Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
3	esv3451660	chr4:147225135-147271246	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	esv3443192	chr4:147225234-147271217	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers ZNF genes & repeats	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	esv3468025	chr4:147225279-147271172	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	esv3468026	chr4:147225279-147271172	Weak transcription ZNF genes & repeats Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	nsv1033640	chr4:147232217-147531881	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:147208400-147254600	Weak transcription	Gastric	stomach
2	chr4:147208600-147254800	Weak transcription	Adipose Nuclei	Adipose
3	chr4:147212800-147264200	Weak transcription	Primary hematopoietic stem cells	blood
4	chr4:147215600-147254800	Weak transcription	Primary T cells from cord blood	blood
5	chr4:147229600-147257400	Weak transcription	Ovary	ovary
6	chr4:147233000-147255000	Weak transcription	Aorta	Aorta
7	chr4:147233200-147254400	Weak transcription	GM12878-XiMat	blood
8	chr4:147241800-147255200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
9	chr4:147241800-147284800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr4:147242800-147255000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
11	chr4:147243000-147255000	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr4:147243200-147254800	Weak transcription	Rectal Mucosa Donor 29	rectum
13	chr4:147244200-147255200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
14	chr4:147246200-147254800	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr4:147246200-147255000	Weak transcription	Primary T helper cells PMA-I stimulated	--
16	chr4:147246400-147254000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr4:147247600-147255000	Weak transcription	Primary T helper cells fromperipheralblood	blood
18	chr4:147248800-147252400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr4:147248800-147257200	Weak transcription	Fetal Intestine Large	intestine
20	chr4:147249000-147252200	Enhancers	NHLF	lung
21	chr4:147249000-147252400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr4:147249000-147252400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr4:147249000-147252400	Enhancers	NHDF-Ad	bronchial
24	chr4:147249000-147252600	Enhancers	HMEC	breast
25	chr4:147249200-147251800	Enhancers	HSMM	muscle
26	chr4:147249200-147252200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr4:147249200-147252400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr4:147249200-147252400	Enhancers	Hela-S3	cervix
29	chr4:147249200-147252600	Enhancers	NHEK	skin
30	chr4:147249400-147251800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr4:147249600-147252200	Enhancers	NH-A	brain
32	chr4:147249600-147252200	Enhancers	Osteobl	bone
33	chr4:147249600-147252400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr4:147249800-147252200	Enhancers	A549	lung
35	chr4:147249800-147253600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr4:147249800-147255400	Weak transcription	Small Intestine	intestine
37	chr4:147249800-147256000	Weak transcription	Lung	lung
38	chr4:147249800-147256400	Weak transcription	Left Ventricle	heart
39	chr4:147249800-147256600	Weak transcription	Esophagus	oesophagus
40	chr4:147250200-147251800	Enhancers	Muscle Satellite Cultured Cells	--
41	chr4:147250400-147254800	Weak transcription	HSMMtube	muscle
42	chr4:147250600-147255000	Weak transcription	Primary monocytes fromperipheralblood	blood
43	chr4:147250800-147251600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr4:147250800-147251800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr4:147251200-147252400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr4:147251400-147251600	Flanking Active TSS	HUVEC	blood vessel
47	chr4:147251400-147254600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr4:147251400-147254600	Weak transcription	Monocytes-CD14+_RO01746	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links