Variant report

Variant	rs542798
Chromosome Location	chr9:15356189-15356190
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs2256786	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2447669	0.89[AFR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2490866	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2798700	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2798725	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2798732	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2804991	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2805011	0.80[EUR][1000 genomes]
rs2849051	0.89[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs2996231	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs516907	0.89[AFR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs517955	0.89[AFR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs518891	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs519761	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs541183	0.89[AFR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs542734	0.80[EUR][1000 genomes]
rs543323	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs562092	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs581994	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs627380	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs635431	0.80[EUR][1000 genomes]
rs639417	0.80[EUR][1000 genomes]
rs648854	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs681093	0.89[AFR][1000 genomes];0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv892624	chr9:15283761-15415461	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv517975	chr9:15286446-15534070	Weak transcription Genic enhancers Active TSS Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv613650	chr9:15296119-15378449	Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv613651	chr9:15296355-15358157	Flanking Active TSS Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv1015960	chr9:15296783-15380657	ZNF genes & repeats Flanking Active TSS Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv524849	chr9:15299590-15362057	Flanking Active TSS Active TSS Enhancers Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
7	nsv892625	chr9:15326251-16064850	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
8	nsv1030287	chr9:15332709-15458001	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:15349000-15357600	Enhancers	HepG2	liver
2	chr9:15350200-15356800	Weak transcription	Rectal Mucosa Donor 29	rectum
3	chr9:15351400-15356800	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr9:15351600-15357200	Weak transcription	Thymus	Thymus
5	chr9:15353600-15357400	Enhancers	Primary hematopoietic stem cells short term culture	blood
6	chr9:15354000-15356200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr9:15354000-15356200	Enhancers	iPS-18 Cell Line	embryonic stem cell
8	chr9:15354000-15357600	Enhancers	Primary T cells from cord blood	blood
9	chr9:15354200-15356200	Enhancers	H1 Cell Line	embryonic stem cell
10	chr9:15354200-15356200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr9:15354600-15356200	Enhancers	HUES48 Cell Line	embryonic stem cell
12	chr9:15354600-15356200	Enhancers	HUES6 Cell Line	embryonic stem cell
13	chr9:15354600-15357600	Enhancers	Primary hematopoietic stem cells	blood
14	chr9:15354800-15356200	Enhancers	Primary T helper cells PMA-I stimulated	--
15	chr9:15355200-15356200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
16	chr9:15355200-15358400	Enhancers	Fetal Intestine Small	intestine
17	chr9:15355400-15356400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr9:15355400-15358600	Enhancers	Fetal Intestine Large	intestine
19	chr9:15355600-15356600	Weak transcription	Primary T helper cells fromperipheralblood	blood
20	chr9:15355600-15356600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr9:15355600-15357200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
22	chr9:15355800-15356200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
23	chr9:15355800-15356400	Enhancers	H9 Cell Line	embryonic stem cell
24	chr9:15355800-15356800	Weak transcription	HUES64 Cell Line	embryonic stem cell
25	chr9:15355800-15356800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
26	chr9:15356000-15356200	Enhancers	Sigmoid Colon	Sigmoid Colon
27	chr9:15356000-15357000	Weak transcription	Fetal Thymus	thymus
28	chr9:15356000-15357200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
29	chr9:15356000-15357200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr9:15356000-15357200	Weak transcription	Primary T cells fromperipheralblood	blood

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