Variant report

Variant	rs2659519
Chromosome Location	chr4:102138899-102138900
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	chr4:102132632..102134649-chr4:102137778..102139733,2	MCF-7	breast:
2	chr4:102134665..102137558-chr4:102138391..102140699,2	MCF-7	breast:

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

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs1157038	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1395474	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1472825	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2135608	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2135609	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2135612	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2659516	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2659517	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2659518	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2659520	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2659521	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2659522	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2659523	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2659525	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2659527	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2659529	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2659530	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2659531	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2850347	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2850365	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2850373	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2850951	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2850972	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2850996	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2850998	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2850999	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2851001	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2851002	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2851003	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2851009	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs67445056	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs970071	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[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	nsv931418	chr4:101500167-102443207	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv999741	chr4:102009017-102454115	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
3	nsv537199	chr4:102009017-102454115	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
4	nsv1004766	chr4:102009017-102713765	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
5	nsv537200	chr4:102009017-102713765	Weak transcription Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
6	nsv1011351	chr4:102056024-102450302	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:102129000-102140400	Weak transcription	Primary T helper cells PMA-I stimulated	--
2	chr4:102131800-102146000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr4:102133000-102143800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr4:102133000-102143800	Weak transcription	Colon Smooth Muscle	Colon
5	chr4:102133200-102142400	Weak transcription	HSMM	muscle
6	chr4:102133200-102143600	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr4:102133400-102139000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
8	chr4:102133800-102139000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr4:102135800-102145200	Weak transcription	Small Intestine	intestine
10	chr4:102136000-102141600	Weak transcription	Stomach Mucosa	stomach
11	chr4:102136000-102144400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
12	chr4:102136000-102145800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
13	chr4:102137400-102140000	Weak transcription	Pancreatic Islets	Pancreatic Islet
14	chr4:102137800-102139200	Enhancers	Ovary	ovary
15	chr4:102138200-102139600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr4:102138200-102140400	Enhancers	NHDF-Ad	bronchial
17	chr4:102138400-102140200	Enhancers	Muscle Satellite Cultured Cells	--
18	chr4:102138400-102140600	Enhancers	Osteobl	bone
19	chr4:102138400-102141200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr4:102138400-102144800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr4:102138600-102139000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr4:102138600-102139200	Enhancers	HUES48 Cell Line	embryonic stem cell
23	chr4:102138600-102139400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr4:102138600-102139400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
25	chr4:102138600-102139600	Enhancers	NH-A	brain
26	chr4:102138600-102140600	Enhancers	HUVEC	blood vessel
27	chr4:102138800-102139000	Weak transcription	Fetal Intestine Large	intestine
28	chr4:102138800-102139200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr4:102138800-102139200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr4:102138800-102139200	Enhancers	Rectal Mucosa Donor 29	rectum
31	chr4:102138800-102139400	Enhancers	Sigmoid Colon	Sigmoid Colon
32	chr4:102138800-102139400	Flanking Active TSS	A549	lung
33	chr4:102138800-102139600	Weak transcription	Brain Inferior Temporal Lobe	brain
34	chr4:102138800-102139800	Enhancers	iPS-20b Cell Line	embryonic stem cell
35	chr4:102138800-102140200	Enhancers	Brain Cingulate Gyrus	brain
36	chr4:102138800-102140200	Enhancers	NHLF	lung
37	chr4:102138800-102140400	Enhancers	Brain Substantia Nigra	brain
38	chr4:102138800-102140400	Enhancers	Rectal Mucosa Donor 31	rectum
39	chr4:102138800-102140600	Enhancers	Brain Anterior Caudate	brain

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