Variant report

Variant	rs17402238
Chromosome Location	chr5:106631692-106631693
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 52 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10058308	0.83[EUR][1000 genomes]
rs10062445	0.83[EUR][1000 genomes]
rs10077806	0.83[EUR][1000 genomes]
rs10515370	1.00[ASN][1000 genomes]
rs10515372	0.94[AFR][1000 genomes];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11948860	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13163748	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13165897	1.00[ASN][1000 genomes]
rs13167605	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13169680	0.94[AFR][1000 genomes];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13179809	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13179824	0.83[EUR][1000 genomes]
rs13184636	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs13184643	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13184806	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs13186418	1.00[ASN][1000 genomes]
rs17159641	1.00[ASN][1000 genomes]
rs17159693	0.81[EUR][1000 genomes]
rs17159727	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17159745	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17159751	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17343335	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17343762	1.00[ASN][1000 genomes]
rs17400404	1.00[ASN][1000 genomes]
rs17403350	1.00[ASN][1000 genomes]
rs1895462	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35307227	0.83[EUR][1000 genomes]
rs35709847	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35740714	1.00[ASN][1000 genomes]
rs35748495	1.00[ASN][1000 genomes]
rs35775035	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55849939	1.00[ASN][1000 genomes]
rs56283997	1.00[ASN][1000 genomes]
rs56852743	0.83[EUR][1000 genomes]
rs60635486	1.00[ASN][1000 genomes]
rs6596736	0.83[EUR][1000 genomes]
rs66460437	1.00[ASN][1000 genomes]
rs67504033	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67878207	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6897756	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72784111	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72784113	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs765075	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7701101	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7711216	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7735115	0.84[EUR][1000 genomes]
rs9327996	0.83[EUR][1000 genomes]
rs9327997	0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1030118	chr5:106006097-106847949	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
2	nsv823170	chr5:106326293-106673695	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv1034276	chr5:106461538-106944163	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
4	nsv537851	chr5:106461538-106944163	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:106621800-106636600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr5:106629600-106632400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
3	chr5:106629600-106632600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr5:106629800-106632600	Enhancers	HUES6 Cell Line	embryonic stem cell
5	chr5:106630400-106631800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr5:106630600-106632600	Enhancers	Ovary	ovary
7	chr5:106631000-106631800	Weak transcription	Stomach Mucosa	stomach
8	chr5:106631200-106632000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
9	chr5:106631200-106632200	Enhancers	ES-I3 Cell Line	embryonic stem cell
10	chr5:106631400-106632000	Enhancers	Primary hematopoietic stem cells	blood
11	chr5:106631400-106632600	Enhancers	iPS-15b Cell Line	embryonic stem cell
12	chr5:106631400-106632600	Enhancers	GM12878-XiMat	blood
13	chr5:106631600-106631800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr5:106631600-106632000	Enhancers	Primary T cells fromperipheralblood	blood
15	chr5:106631600-106632000	Enhancers	Cortex derived primary cultured neurospheres	brain
16	chr5:106631600-106632200	Enhancers	HUES64 Cell Line	embryonic stem cell
17	chr5:106631600-106632200	Enhancers	iPS-18 Cell Line	embryonic stem cell
18	chr5:106631600-106632600	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr5:106631600-106636400	Weak transcription	HUES48 Cell Line	embryonic stem cell

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