Variant report

Variant	rs62289276
Chromosome Location	chr4:7800754-7800755
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	chr4:7799366..7802066-chr4:7938906..7941900,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000196526	Chromatin interaction
ENSG00000228919	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs11721583	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11721609	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11724632	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11728778	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11729332	0.91[EUR][1000 genomes]
rs11729602	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11730169	0.84[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs11731942	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11733311	0.86[EUR][1000 genomes]
rs11734524	0.89[EUR][1000 genomes]
rs11734860	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11737447	0.88[EUR][1000 genomes]
rs13113113	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13117918	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13125295	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13132939	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17382379	0.88[EUR][1000 genomes]
rs17382393	0.89[EUR][1000 genomes]
rs17466895	0.88[EUR][1000 genomes]
rs34250310	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs34276892	0.81[EUR][1000 genomes]
rs34352176	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs34949259	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs35041036	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs35161247	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs35509185	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs35515779	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs35592594	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35617438	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs35870249	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35889107	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3934645	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs41264705	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4443284	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4594724	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs55698135	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs55740648	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56270003	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56352084	0.86[EUR][1000 genomes]
rs58457272	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61036795	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62289280	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62291980	0.88[EUR][1000 genomes]
rs62291983	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62291984	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs885260	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs885261	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv878570	chr4:7534603-7836835	Bivalent Enhancer Flanking Active TSS Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
2	nsv491712	chr4:7582506-8155069	Enhancers Bivalent Enhancer Genic enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
3	nsv1007319	chr4:7705550-7832097	Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
4	nsv537018	chr4:7705550-7832097	Genic enhancers Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
5	nsv1006642	chr4:7786980-7811291	Strong transcription Weak transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	esv34140	chr4:7787936-8172491	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:7762000-7805800	Weak transcription	Stomach Mucosa	stomach
2	chr4:7770800-7828400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr4:7776400-7806800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr4:7781400-7801000	Weak transcription	Brain Substantia Nigra	brain
5	chr4:7781400-7801200	Weak transcription	Brain Anterior Caudate	brain
6	chr4:7781600-7807400	Weak transcription	Brain Angular Gyrus	brain
7	chr4:7783800-7806200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
8	chr4:7784000-7801800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
9	chr4:7784000-7821200	Weak transcription	Small Intestine	intestine
10	chr4:7784200-7802200	Weak transcription	Aorta	Aorta
11	chr4:7784200-7802800	Strong transcription	Fetal Muscle Trunk	muscle
12	chr4:7784800-7803400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr4:7785800-7803800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
14	chr4:7786000-7800800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr4:7787000-7829400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
16	chr4:7789200-7806600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr4:7790800-7800800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
18	chr4:7790800-7803600	Strong transcription	HSMM	muscle
19	chr4:7791000-7801400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr4:7791000-7806600	Weak transcription	Psoas Muscle	Psoas
21	chr4:7791000-7829400	Weak transcription	Primary monocytes fromperipheralblood	blood
22	chr4:7791200-7800800	Weak transcription	Spleen	Spleen
23	chr4:7791400-7806600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr4:7791600-7801200	Weak transcription	Fetal Brain Male	brain
25	chr4:7792200-7803200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr4:7792600-7802800	Strong transcription	ES-I3 Cell Line	embryonic stem cell
27	chr4:7792600-7803400	Strong transcription	A549	lung
28	chr4:7792800-7803000	Strong transcription	HSMMtube	muscle
29	chr4:7793200-7803800	Strong transcription	NH-A	brain
30	chr4:7794400-7803600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
31	chr4:7794800-7803400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr4:7795600-7803800	Weak transcription	Fetal Kidney	kidney
33	chr4:7795800-7803800	Weak transcription	Fetal Heart	heart
34	chr4:7796000-7803400	Strong transcription	HUVEC	blood vessel
35	chr4:7796600-7803400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr4:7796800-7804200	Strong transcription	NHEK	skin
37	chr4:7797000-7807000	Weak transcription	Liver	Liver
38	chr4:7797200-7803000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr4:7797200-7803800	Strong transcription	Muscle Satellite Cultured Cells	--
40	chr4:7797600-7802400	Strong transcription	Placenta Amnion	Placenta Amnion
41	chr4:7797600-7802800	Strong transcription	Rectal Mucosa Donor 29	rectum
42	chr4:7797600-7803000	Strong transcription	HUES6 Cell Line	embryonic stem cell
43	chr4:7797600-7803200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
44	chr4:7797600-7803200	Strong transcription	Fetal Stomach	stomach
45	chr4:7797800-7802800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr4:7797800-7802800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr4:7797800-7802800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
48	chr4:7797800-7802800	Strong transcription	Placenta	Placenta
49	chr4:7797800-7803000	Strong transcription	NHLF	lung
50	chr4:7797800-7803200	Strong transcription	NHDF-Ad	bronchial

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