Variant report

Variant	rs233128
Chromosome Location	chr1:85794413-85794414
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	chr1:85783416..85785101-chr1:85792646..85795360,2	MCF-7	breast:

Extended variants
information (count: 14 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs10782548	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11587876	0.88[JPT][hapmap]
rs17127710	0.80[CHB][hapmap]
rs233046	0.85[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs233051	0.90[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs233080	0.91[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs233087	0.89[ASN][1000 genomes]
rs233111	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34278923	0.81[ASN][1000 genomes]
rs591917	0.90[CEU][hapmap]
rs648216	0.90[CEU][hapmap]
rs7532508	0.90[CEU][hapmap];0.82[CHB][hapmap];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1006994	chr1:85454304-86327679	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	esv34165	chr1:85542040-85846249	Flanking Active TSS Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:79 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:85774600-85794800	Weak transcription	Spleen	Spleen
2	chr1:85780000-85795800	Weak transcription	Rectal Smooth Muscle	rectum
3	chr1:85780200-85795800	Weak transcription	Stomach Smooth Muscle	stomach
4	chr1:85780400-85795800	Weak transcription	Gastric	stomach
5	chr1:85782400-85795000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr1:85782800-85794600	Weak transcription	Skeletal Muscle Female	skeletal muscle
7	chr1:85783000-85795800	Weak transcription	Rectal Mucosa Donor 29	rectum
8	chr1:85783200-85795800	Weak transcription	Aorta	Aorta
9	chr1:85784000-85794600	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr1:85784600-85794600	Weak transcription	Fetal Lung	lung
11	chr1:85788600-85797400	Weak transcription	Fetal Muscle Trunk	muscle
12	chr1:85789400-85795800	Weak transcription	Liver	Liver
13	chr1:85789600-85794600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr1:85789800-85795800	Weak transcription	Fetal Stomach	stomach
15	chr1:85789800-85795800	Weak transcription	Lung	lung
16	chr1:85790000-85795600	Enhancers	NHDF-Ad	bronchial
17	chr1:85790200-85795200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr1:85790400-85795600	Weak transcription	Brain Germinal Matrix	brain
19	chr1:85790400-85796200	Enhancers	ES-I3 Cell Line	embryonic stem cell
20	chr1:85790400-85797000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr1:85790600-85800000	Enhancers	HUVEC	blood vessel
22	chr1:85790800-85794600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr1:85791000-85794600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr1:85791000-85796800	Enhancers	HepG2	liver
25	chr1:85791200-85794800	Weak transcription	Cortex derived primary cultured neurospheres	brain
26	chr1:85791200-85798000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr1:85791400-85794600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
28	chr1:85791400-85794800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr1:85791400-85797400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr1:85791800-85794600	Weak transcription	Fetal Intestine Large	intestine
31	chr1:85792000-85794600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
32	chr1:85792000-85795400	Weak transcription	Placenta Amnion	Placenta Amnion
33	chr1:85792000-85795800	Weak transcription	Duodenum Smooth Muscle	Duodenum
34	chr1:85792200-85795600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
35	chr1:85792200-85796400	Weak transcription	Duodenum Mucosa	Duodenum
36	chr1:85792200-85806000	Weak transcription	Fetal Kidney	kidney
37	chr1:85792400-85796200	Weak transcription	Rectal Mucosa Donor 31	rectum
38	chr1:85792600-85794800	Weak transcription	Stomach Mucosa	stomach
39	chr1:85792600-85795600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr1:85792600-85797800	Weak transcription	Fetal Intestine Small	intestine
41	chr1:85792800-85796600	Enhancers	HUES48 Cell Line	embryonic stem cell
42	chr1:85793000-85797000	Enhancers	HMEC	breast
43	chr1:85793200-85797000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr1:85793200-85797600	Enhancers	NHEK	skin
45	chr1:85793200-85798600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr1:85793400-85794600	Weak transcription	Pancreas	Pancrea
47	chr1:85793400-85795000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr1:85793400-85797600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr1:85793600-85795800	Enhancers	Muscle Satellite Cultured Cells	--
50	chr1:85793600-85795800	Weak transcription	Colon Smooth Muscle	Colon

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