Variant report

Variant	rs17398264
Chromosome Location	chr1:80998603-80998604
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CHD1	chr1:80998537-80998660	H1-hESC	embryonic stem cell:	n/a	n/a

Variant related genes	Relation type
ENSG00000234184	TF binding region

Extended variants
information (count: 30 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs11800144	0.91[EUR][1000 genomes]
rs11803485	0.91[EUR][1000 genomes]
rs11808487	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17394147	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17398419	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17398515	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17398889	0.88[AFR][1000 genomes]
rs61774396	0.91[EUR][1000 genomes]
rs61774404	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61774405	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61774408	0.88[AFR][1000 genomes]
rs74098359	0.95[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:18 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1012286	chr1:80057078-81005153	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv535018	chr1:80057078-81005153	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
3	nsv1000792	chr1:80076146-81015283	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
4	nsv546661	chr1:80656114-81156849	Enhancers Flanking Active TSS Genic enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
5	nsv462284	chr1:80888808-81042755	Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
6	nsv546665	chr1:80888808-81042755	Enhancers ZNF genes & repeats Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
7	esv2754595	chr1:80906634-81214971	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
8	nsv462295	chr1:80909417-81052058	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
9	nsv546666	chr1:80909417-81052058	Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
10	nsv462306	chr1:80926312-81042755	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
11	nsv546667	chr1:80926312-81042755	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
12	nsv1008699	chr1:80950333-81008134	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
13	nsv462317	chr1:80964490-81052058	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
14	nsv462328	chr1:80964490-81052058	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
15	nsv546668	chr1:80964490-81052058	Enhancers Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
16	nsv871193	chr1:80970978-81056946	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
17	nsv871285	chr1:80996970-81071433	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
18	nsv871748	chr1:80996970-81329765	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:80997000-80999400	Enhancers	iPS-18 Cell Line	embryonic stem cell
2	chr1:80997400-81000600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr1:80998000-81001800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr1:80998200-80998800	Weak transcription	Colon Smooth Muscle	Colon
5	chr1:80998400-80999200	Enhancers	HUES64 Cell Line	embryonic stem cell
6	chr1:80998400-80999400	Enhancers	HUES48 Cell Line	embryonic stem cell
7	chr1:80998400-80999400	Enhancers	iPS-20b Cell Line	embryonic stem cell
8	chr1:80998400-80999400	Enhancers	Brain Germinal Matrix	brain
9	chr1:80998400-81000200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr1:80998400-81001000	Enhancers	Breast Myoepithelial Primary Cells	Breast
11	chr1:80998600-80998800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
12	chr1:80998600-80998800	Active TSS	A549	lung
13	chr1:80998600-80999400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr1:80998600-80999400	Enhancers	Cortex derived primary cultured neurospheres	brain
15	chr1:80998600-81000000	Enhancers	H9 Cell Line	embryonic stem cell
16	chr1:80998600-81000000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr1:80998600-81000000	Enhancers	Fetal Kidney	kidney
18	chr1:80998600-81000800	Enhancers	H1 Cell Line	embryonic stem cell
19	chr1:80998600-81000800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
20	chr1:80998600-81001600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr1:80998600-81003400	Enhancers	ES-I3 Cell Line	embryonic stem cell
22	chr1:80998600-81003600	Enhancers	HUES6 Cell Line	embryonic stem cell
23	chr1:80998600-81003600	Enhancers	iPS-15b Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links