Variant report

Variant	rs4495663
Chromosome Location	chr1:227559090-227559091
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:227503449..227507598-chr1:227555312..227559428,5	K562	blood:
2	chr1:227503449..227507598-chr1:227555312..227559110,4	K562	blood:
3	chr1:227554602..227556640-chr1:227558228..227560201,2	K562	blood:
4	chr1:227554260..227555782-chr1:227558774..227561008,2	K562	blood:
5	chr1:227545277..227548710-chr1:227557152..227561579,4	K562	blood:
6	chr1:227544961..227546777-chr1:227556862..227559703,3	K562	blood:
7	chr1:227556870..227561275-chr1:227563192..227568675,6	K562	blood:
8	chr1:227519023..227520761-chr1:227558780..227560825,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000143776	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs11799772	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11802810	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11808370	1.00[AMR][1000 genomes]
rs11810240	0.85[AMR][1000 genomes]
rs11811413	0.85[AMR][1000 genomes]
rs16847771	1.00[MEX][hapmap];0.85[AMR][1000 genomes]
rs34942855	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs56339347	0.98[AFR][1000 genomes]
rs56897207	1.00[AMR][1000 genomes]
rs58582199	0.85[AMR][1000 genomes]
rs59198448	0.85[AMR][1000 genomes]
rs61510060	0.83[AMR][1000 genomes]
rs6688385	0.82[YRI][hapmap];1.00[AMR][1000 genomes]
rs6696713	0.86[ASW][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.82[YRI][hapmap];1.00[AMR][1000 genomes]
rs6699740	1.00[AMR][1000 genomes]
rs73102326	1.00[AMR][1000 genomes]
rs73102327	1.00[AMR][1000 genomes]
rs73102341	1.00[AMR][1000 genomes]
rs73102365	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73102377	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73102383	0.85[AMR][1000 genomes]
rs74140179	0.85[AMR][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	nsv1003656	chr1:227034700-227559665	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv535318	chr1:227034700-227559665	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
3	nsv534002	chr1:227315186-228047108	Bivalent/Poised TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases
4	nsv873242	chr1:227371906-227579344	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
5	nsv549271	chr1:227411003-227581017	Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
6	nsv1001353	chr1:227474785-227660691	Flanking Active TSS Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4495663	PSEN2	cis	lymphoblastoid	seeQTL
rs4495663	CDC42BPA	cis	lymphoblastoid	seeQTL
rs4495663	LMO2	trans	lymphoblastoid	seeQTL

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:227545800-227571200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr1:227556600-227559200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr1:227556800-227560800	Enhancers	Pancreatic Islets	Pancreatic Islet
4	chr1:227556800-227560800	Enhancers	Stomach Mucosa	stomach
5	chr1:227556800-227561200	Enhancers	Muscle Satellite Cultured Cells	--
6	chr1:227556800-227561200	Enhancers	HUVEC	blood vessel
7	chr1:227557200-227559600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
8	chr1:227557200-227565400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
9	chr1:227558000-227560600	Enhancers	A549	lung
10	chr1:227558200-227560000	Enhancers	K562	blood
11	chr1:227558600-227560000	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr1:227558600-227560000	Weak transcription	HSMM	muscle
13	chr1:227558600-227565400	Weak transcription	HSMMtube	muscle
14	chr1:227558600-227565600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
15	chr1:227558800-227559800	Weak transcription	Brain Hippocampus Middle	brain
16	chr1:227558800-227560000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr1:227558800-227560000	Weak transcription	Cortex derived primary cultured neurospheres	brain
18	chr1:227559000-227559800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr1:227559000-227560200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr1:227559000-227565800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links