Variant report

Variant	rs2464513
Chromosome Location	chr4:89945728-89945729
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:89739441..89740830-chr4:89944929..89945920,11	MCF-7	breast:
2	chr4:89743339..89746307-chr4:89945408..89946959,2	K562	blood:
3	chr4:89739546..89740487-chr4:89944633..89945904,7	MCF-7	breast:
4	chr4:89593853..89594728-chr4:89944932..89945908,3	K562	blood:

Variant related genes	Relation type
ENSG00000138640	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs1060693	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12647382	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13143981	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1398947	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1458558	0.81[ASN][1000 genomes]
rs1513807	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1513824	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1533291	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1708660	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1708661	0.98[ASN][1000 genomes]
rs1708675	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1708678	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1708679	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1708680	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1708682	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1708684	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1795721	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1795728	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1795733	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1807870	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1818494	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2458545	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2609267	0.81[ASN][1000 genomes]
rs2670624	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2670626	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2670629	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2670630	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28498689	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs59610544	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs60535906	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62308652	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6532094	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6846926	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9307062	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs938266	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[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	nsv470051	chr4:89644931-90643144	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv1009354	chr4:89725914-89985155	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
3	nsv1007025	chr4:89837734-90098046	Enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription ZNF genes & repeats Genic enhancers 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 target site	10 gene(s)	inside rSNPs	diseases
4	nsv537176	chr4:89837734-90098046	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
5	nsv461577	chr4:89904124-89986326	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA target site	6 gene(s)	inside rSNPs	diseases
6	nsv594807	chr4:89904124-89986326	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA target site	6 gene(s)	inside rSNPs	diseases
7	nsv1002448	chr4:89933385-90128133	Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Genic enhancers Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:89903000-89957200	Weak transcription	HSMM	muscle
2	chr4:89921000-89950600	Weak transcription	Rectal Mucosa Donor 29	rectum
3	chr4:89922600-89949800	Weak transcription	HMEC	breast
4	chr4:89926400-89949600	Weak transcription	Left Ventricle	heart
5	chr4:89926800-89951400	Weak transcription	Right Ventricle	heart
6	chr4:89933600-89951400	Weak transcription	NHLF	lung
7	chr4:89937200-89975600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr4:89938200-89953000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr4:89939600-89951200	Weak transcription	NHEK	skin
10	chr4:89940200-89949800	Weak transcription	Primary T cells from cord blood	blood
11	chr4:89940200-89957800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr4:89940400-89956600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr4:89940400-89956600	Weak transcription	NH-A	brain
14	chr4:89940400-89957800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr4:89940400-89957800	Weak transcription	Aorta	Aorta
16	chr4:89940400-89959000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr4:89940400-89961000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr4:89940600-89954400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr4:89940600-89956000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr4:89940600-89956000	Weak transcription	Cortex derived primary cultured neurospheres	brain
21	chr4:89940600-89957800	Weak transcription	H1 Cell Line	embryonic stem cell
22	chr4:89940600-89957800	Weak transcription	Ovary	ovary
23	chr4:89940800-89956800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr4:89941200-89956000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
25	chr4:89941200-89956200	Weak transcription	Fetal Lung	lung
26	chr4:89941800-89947800	Weak transcription	Fetal Muscle Leg	muscle
27	chr4:89941800-89948000	Weak transcription	Fetal Muscle Trunk	muscle
28	chr4:89941800-89952200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr4:89941800-89952400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr4:89941800-89952600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr4:89941800-89957800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr4:89941800-89957800	Weak transcription	Fetal Stomach	stomach
33	chr4:89942000-89947800	Weak transcription	HUES64 Cell Line	embryonic stem cell
34	chr4:89942000-89948600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
35	chr4:89942000-89950000	Weak transcription	HUES48 Cell Line	embryonic stem cell
36	chr4:89942000-89951200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
37	chr4:89942200-89949200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr4:89943200-89950600	Weak transcription	Primary T helper cells PMA-I stimulated	--
39	chr4:89943800-89946400	Enhancers	HepG2	liver
40	chr4:89944200-89951000	Weak transcription	Sigmoid Colon	Sigmoid Colon
41	chr4:89944200-89954000	Weak transcription	Small Intestine	intestine
42	chr4:89944200-89958000	Weak transcription	Fetal Heart	heart
43	chr4:89944200-89978000	Weak transcription	Pancreas	Pancrea
44	chr4:89944600-89945800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr4:89944800-89948000	Weak transcription	K562	blood
46	chr4:89944800-89955400	Weak transcription	Skeletal Muscle Female	skeletal muscle
47	chr4:89945000-89945800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr4:89945000-89945800	Enhancers	Colon Smooth Muscle	Colon
49	chr4:89945000-89945800	Enhancers	Fetal Brain Male	brain
50	chr4:89945000-89948600	Weak transcription	Fetal Intestine Large	intestine

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