Variant report

Variant	rs58728331
Chromosome Location	chr4:129747480-129747481
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:129732385..129733951-chr4:129746938..129749737,2	MCF-7	breast:
2	chr4:129731358..129733912-chr4:129746090..129749523,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000077684	Chromatin interaction

Extended variants
information (count: 69 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs17013725	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17013730	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs17013733	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17013736	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17013744	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17013759	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17013765	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17013766	1.00[EUR][1000 genomes]
rs17013775	1.00[EUR][1000 genomes]
rs17013777	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17013779	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17013786	0.95[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs17013787	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17013789	0.95[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs17013807	0.95[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs17013811	0.95[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs17013813	0.95[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs17013815	0.95[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs17013817	0.95[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs17013825	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17013827	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17013835	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17013841	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17013844	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17013847	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17013848	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17013849	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17013852	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17013854	0.95[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs17013857	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17013862	0.85[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs17013866	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17013872	0.85[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs17013873	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17013877	0.85[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs17013882	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17013894	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17013895	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17013898	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17013899	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17013903	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17303098	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2004378	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28635430	1.00[EUR][1000 genomes]
rs57153966	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57547066	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58296567	0.82[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs58580868	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58593491	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58755790	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58922070	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58981205	1.00[EUR][1000 genomes]
rs59682469	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs60787284	1.00[EUR][1000 genomes]
rs61306978	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61620977	1.00[EUR][1000 genomes]
rs61696721	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs6813405	0.85[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs6827804	0.85[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs6848234	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6850940	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6855813	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73846991	1.00[EUR][1000 genomes]
rs73850004	1.00[EUR][1000 genomes]
rs7682356	1.00[AFR][1000 genomes];1.00[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	nsv869258	chr4:129191619-130138148	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases
2	nsv1020801	chr4:129658178-129778086	Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
3	nsv537248	chr4:129658178-129778086	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
4	nsv517249	chr4:129738328-129927804	Genic enhancers Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:129734400-129751600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chr4:129734400-129756400	Weak transcription	Aorta	Aorta
3	chr4:129735400-129748200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr4:129735400-129752200	Weak transcription	Fetal Brain Female	brain
5	chr4:129738600-129749200	Enhancers	Primary T helper cells PMA-I stimulated	--
6	chr4:129740400-129749200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr4:129740800-129748000	Weak transcription	Liver	Liver
8	chr4:129741000-129748600	Weak transcription	Fetal Thymus	thymus
9	chr4:129741200-129748000	Weak transcription	HepG2	liver
10	chr4:129741200-129748200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
11	chr4:129741200-129748400	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr4:129741200-129749400	Enhancers	Primary T helper cells fromperipheralblood	blood
13	chr4:129741200-129749600	Enhancers	NHDF-Ad	bronchial
14	chr4:129741800-129750000	Weak transcription	Psoas Muscle	Psoas
15	chr4:129741800-129752000	Weak transcription	Primary hematopoietic stem cells	blood
16	chr4:129743200-129749800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr4:129743400-129749600	Enhancers	Osteobl	bone
18	chr4:129744000-129748600	Enhancers	HSMM	muscle
19	chr4:129744600-129747600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr4:129744800-129751600	Weak transcription	HUVEC	blood vessel
21	chr4:129745000-129749200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr4:129745000-129751200	Enhancers	iPS-15b Cell Line	embryonic stem cell
23	chr4:129745200-129749800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr4:129745600-129748800	Enhancers	Fetal Intestine Large	intestine
25	chr4:129745600-129749000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
26	chr4:129745600-129749000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr4:129745800-129747600	Enhancers	ES-WA7 Cell Line	embryonic stem cell
28	chr4:129745800-129749600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
29	chr4:129745800-129749800	Enhancers	Fetal Heart	heart
30	chr4:129745800-129749800	Enhancers	NHLF	lung
31	chr4:129746000-129747600	Enhancers	Duodenum Smooth Muscle	Duodenum
32	chr4:129746000-129747600	Enhancers	Skeletal Muscle Female	skeletal muscle
33	chr4:129746000-129748600	Enhancers	Duodenum Mucosa	Duodenum
34	chr4:129746000-129749000	Enhancers	Fetal Intestine Small	intestine
35	chr4:129746000-129749000	Weak transcription	Pancreatic Islets	Pancreatic Islet
36	chr4:129746000-129749600	Genic enhancers	iPS-18 Cell Line	embryonic stem cell
37	chr4:129746000-129750200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr4:129746200-129747600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
39	chr4:129746200-129747800	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr4:129746200-129748000	Enhancers	Lung	lung
41	chr4:129746200-129748800	Enhancers	Ovary	ovary
42	chr4:129746200-129749200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr4:129746200-129749200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr4:129746200-129749200	Enhancers	Pancreas	Pancrea
45	chr4:129746200-129749200	Enhancers	Right Atrium	heart
46	chr4:129746200-129749800	Enhancers	Adipose Nuclei	Adipose
47	chr4:129746200-129750000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
48	chr4:129746200-129750400	Enhancers	Left Ventricle	heart
49	chr4:129746400-129747600	Genic enhancers	H9 Cell Line	embryonic stem cell
50	chr4:129746400-129747600	Genic enhancers	Primary hematopoietic stem cells short term culture	blood

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