Variant report

Variant	rs28425587
Chromosome Location	chr4:7909401-7909402
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:7907878..7909854-chr4:7910012..7912974,3	MCF-7	breast:

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10005650	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10024625	0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2386054	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs28434072	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28498817	0.93[EUR][1000 genomes]
rs28607438	0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28668205	0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28675899	0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28735181	0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28735634	0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28842326	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4401450	0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4478172	0.95[ASN][1000 genomes]
rs4488938	0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs61081420	0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs61214925	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6605361	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6820041	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6839086	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6842743	1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs71175434	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs73073924	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73088591	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs73088594	0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs73090508	0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs73090513	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs73090514	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7376703	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7676488	0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7691757	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7695510	0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9330346	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9654093	0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	esv2754386	chr4:7822449-7992909	Weak transcription Enhancers Active TSS Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	esv2756298	chr4:7822449-7992909	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv878578	chr4:7841833-7969594	Enhancers Flanking Active TSS Genic enhancers Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:7894200-7912400	Weak transcription	Fetal Intestine Large	intestine
2	chr4:7899800-7930600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr4:7900200-7912400	Weak transcription	NHEK	skin
4	chr4:7900800-7914400	Enhancers	ES-I3 Cell Line	embryonic stem cell
5	chr4:7901600-7914400	Enhancers	Fetal Muscle Leg	muscle
6	chr4:7903400-7911400	Weak transcription	Pancreas	Pancrea
7	chr4:7903400-7911600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr4:7903600-7915000	Enhancers	Fetal Stomach	stomach
9	chr4:7904600-7910000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
10	chr4:7904600-7910400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
11	chr4:7904600-7910400	Weak transcription	Primary T helper cells fromperipheralblood	blood
12	chr4:7904800-7910000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
13	chr4:7904800-7910400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
14	chr4:7904800-7911200	Weak transcription	Gastric	stomach
15	chr4:7904800-7912200	Weak transcription	Duodenum Mucosa	Duodenum
16	chr4:7905000-7911200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
17	chr4:7905200-7911200	Weak transcription	Small Intestine	intestine
18	chr4:7905200-7911800	Weak transcription	Aorta	Aorta
19	chr4:7905600-7912400	Enhancers	HUES6 Cell Line	embryonic stem cell
20	chr4:7906000-7911000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr4:7906000-7914200	Enhancers	Cortex derived primary cultured neurospheres	brain
22	chr4:7906200-7909800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr4:7906200-7911600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr4:7906200-7914400	Enhancers	HUVEC	blood vessel
25	chr4:7907000-7912400	Weak transcription	Left Ventricle	heart
26	chr4:7907400-7909600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr4:7907800-7911000	Weak transcription	Colonic Mucosa	Colon
28	chr4:7907800-7911200	Weak transcription	Rectal Mucosa Donor 31	rectum
29	chr4:7907800-7911400	Weak transcription	Lung	lung
30	chr4:7907800-7911600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr4:7907800-7911600	Weak transcription	Esophagus	oesophagus
32	chr4:7907800-7911800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
33	chr4:7907800-7912200	Weak transcription	Brain Substantia Nigra	brain
34	chr4:7907800-7912200	Weak transcription	Rectal Mucosa Donor 29	rectum
35	chr4:7907800-7914200	Enhancers	Brain Germinal Matrix	brain
36	chr4:7907800-7935800	Weak transcription	Right Ventricle	heart
37	chr4:7908000-7909600	Enhancers	NH-A	brain
38	chr4:7908000-7910600	Genic enhancers	HSMM	muscle
39	chr4:7908000-7911200	Weak transcription	Brain Inferior Temporal Lobe	brain
40	chr4:7908000-7911200	Weak transcription	Sigmoid Colon	Sigmoid Colon
41	chr4:7908000-7911400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
42	chr4:7908000-7911400	Weak transcription	H1 Cell Line	embryonic stem cell
43	chr4:7908000-7911400	Weak transcription	Brain Cingulate Gyrus	brain
44	chr4:7908000-7911400	Weak transcription	Brain Hippocampus Middle	brain
45	chr4:7908000-7911400	Weak transcription	Fetal Brain Male	brain
46	chr4:7908000-7911400	Enhancers	NHDF-Ad	bronchial
47	chr4:7908000-7911800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
48	chr4:7908000-7911800	Enhancers	Colon Smooth Muscle	Colon
49	chr4:7908000-7912200	Weak transcription	Skeletal Muscle Female	skeletal muscle
50	chr4:7908000-7912600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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