Variant report

Variant	rs9660988
Chromosome Location	chr1:153548294-153548295
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:153547912..153551190-chr1:153580716..153583524,6	MCF-7	breast:
2	chr1:153548198..153549915-chr1:153576561..153578484,2	K562	blood:
3	chr1:153533881..153554060-chr1:153575339..153590405,58	MCF-7	breast:
4	chr1:153548195..153551258-chr1:153612052..153615692,3	MCF-7	breast:
5	chr1:153539127..153551919-chr1:153598146..153608314,34	MCF-7	breast:
6	chr1:153547134..153549764-chr1:153700485..153703483,2	MCF-7	breast:
7	chr1:153547283..153551329-chr1:153605109..153608605,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000189171	Chromatin interaction
ENSG00000272030	Chromatin interaction
ENSG00000160679	Chromatin interaction
ENSG00000271853	Chromatin interaction
ENSG00000143624	Chromatin interaction
ENSG00000189334	Chromatin interaction
ENSG00000188643	Chromatin interaction
ENSG00000160678	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs28636749	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs28715047	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes]
rs55815414	0.84[EUR][1000 genomes]
rs55963294	0.84[EUR][1000 genomes]
rs9662163	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9662917	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1010488	chr1:152901263-153670972	Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	236 gene(s)	inside rSNPs	diseases
2	nsv535171	chr1:152901263-153670972	Enhancers Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	236 gene(s)	inside rSNPs	diseases
3	nsv831603	chr1:153405842-153576143	Transcr. at gene 5' and 3' Bivalent Enhancer Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	148 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:153539600-153554000	Weak transcription	Ovary	ovary
2	chr1:153541600-153550200	Weak transcription	Right Atrium	heart
3	chr1:153541800-153549400	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr1:153544400-153548800	Weak transcription	Placenta	Placenta
5	chr1:153544600-153549400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr1:153545000-153550200	Weak transcription	Esophagus	oesophagus
7	chr1:153545200-153550200	Weak transcription	Fetal Muscle Trunk	muscle
8	chr1:153545400-153550200	Weak transcription	Brain Anterior Caudate	brain
9	chr1:153545600-153548400	Weak transcription	HepG2	liver
10	chr1:153545600-153549600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr1:153545800-153549600	Weak transcription	Duodenum Mucosa	Duodenum
12	chr1:153545800-153551400	Weak transcription	Spleen	Spleen
13	chr1:153546000-153549600	Weak transcription	Primary B cells from peripheral blood	blood
14	chr1:153546000-153549600	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr1:153546000-153549800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr1:153546000-153549800	Weak transcription	Fetal Muscle Leg	muscle
17	chr1:153546000-153549800	Weak transcription	A549	lung
18	chr1:153546000-153556600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr1:153546200-153548600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr1:153546200-153549400	Weak transcription	HSMMtube	muscle
21	chr1:153546200-153549600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr1:153546200-153549600	Weak transcription	Hela-S3	cervix
23	chr1:153546200-153549800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr1:153546200-153549800	Weak transcription	Primary B cells from cord blood	blood
25	chr1:153546200-153549800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr1:153546200-153549800	Weak transcription	Muscle Satellite Cultured Cells	--
27	chr1:153546200-153549800	Weak transcription	HSMM	muscle
28	chr1:153546200-153549800	Weak transcription	NHDF-Ad	bronchial
29	chr1:153546200-153549800	Weak transcription	NHLF	lung
30	chr1:153546200-153549800	Weak transcription	Osteobl	bone
31	chr1:153546200-153550200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr1:153546200-153550200	Weak transcription	HMEC	breast
33	chr1:153546200-153550400	Weak transcription	Cortex derived primary cultured neurospheres	brain
34	chr1:153546200-153550400	Weak transcription	Adipose Nuclei	Adipose
35	chr1:153546400-153548800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr1:153546400-153549400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr1:153546600-153549400	Weak transcription	Primary monocytes fromperipheralblood	blood
38	chr1:153546600-153549400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr1:153546600-153549800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr1:153546600-153549800	Weak transcription	Monocytes-CD14+_RO01746	blood
41	chr1:153546800-153549400	Weak transcription	Primary neutrophils fromperipheralblood	blood
42	chr1:153546800-153549600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr1:153546800-153550200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr1:153546800-153556600	Weak transcription	NH-A	brain
45	chr1:153547000-153548600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr1:153547000-153549400	Weak transcription	NHEK	skin
47	chr1:153548000-153550400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links