Variant report

Variant	rs56103229
Chromosome Location	chr1:220471743-220471744
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	chr1:220469913..220472006-chr1:220498061..220500308,2	MCF-7	breast:
2	chr1:220471708..220473237-chr1:220473384..220475197,2	K562	blood:

Extended variants
information (count: 27 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs17565738	0.86[AMR][1000 genomes]
rs17565935	0.95[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs17566172	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17567252	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17641091	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17641428	0.85[ASN][1000 genomes]
rs55673394	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs55807644	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55914754	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55991348	0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs56040283	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56129807	0.81[AMR][1000 genomes]
rs72730664	0.81[AMR][1000 genomes]
rs72730666	0.81[AMR][1000 genomes]
rs72730668	0.81[AMR][1000 genomes]
rs72749215	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72749218	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72749219	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72749221	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72749222	0.95[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs72749226	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72749236	0.88[ASN][1000 genomes]
rs7519416	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7520639	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7521141	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[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	nsv1001681	chr1:220425057-220548325	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv535298	chr1:220425057-220548325	Weak transcription Strong transcription Genic enhancers Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs56103229	RP11-392O17.1	cis	Artery Tibial	GTEx

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:220464200-220473600	Weak transcription	HUES6 Cell Line	embryonic stem cell
2	chr1:220464600-220473800	Weak transcription	HUES64 Cell Line	embryonic stem cell
3	chr1:220465200-220472600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr1:220467400-220472200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr1:220468400-220473600	Weak transcription	Rectal Smooth Muscle	rectum
6	chr1:220468600-220473400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr1:220468600-220473400	Weak transcription	NH-A	brain
8	chr1:220468600-220473600	Weak transcription	Muscle Satellite Cultured Cells	--
9	chr1:220468600-220473600	Weak transcription	Fetal Stomach	stomach
10	chr1:220469200-220473400	Weak transcription	NHDF-Ad	bronchial
11	chr1:220470000-220472200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr1:220470600-220472000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr1:220470800-220473400	Weak transcription	Osteobl	bone
14	chr1:220470800-220473600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr1:220471200-220472800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr1:220471200-220473200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr1:220471200-220473800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr1:220471400-220473000	Enhancers	ES-I3 Cell Line	embryonic stem cell
19	chr1:220471400-220473600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr1:220471600-220472400	Enhancers	iPS-20b Cell Line	embryonic stem cell
21	chr1:220471600-220472600	Enhancers	iPS-15b Cell Line	embryonic stem cell
22	chr1:220471600-220472600	Enhancers	iPS-18 Cell Line	embryonic stem cell
23	chr1:220471600-220472600	Enhancers	Brain Germinal Matrix	brain
24	chr1:220471600-220473800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr1:220471600-220474000	Enhancers	Cortex derived primary cultured neurospheres	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links