Variant report

Variant	rs12004877
Chromosome Location	chr9:15356919-15356920
allele	C/T
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	CTCF	chr9:15356880-15357030	GM12867	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:15277443..15278337-chr9:15356714..15357650,2	MCF-7	breast:
2	chr9:15211338..15211919-chr9:15356761..15357369,2	MCF-7	breast:

Variant related genes	Relation type
RPL7P33	TF binding region

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10810376	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10961975	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10961976	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10961977	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs473315	0.94[CHB][hapmap]
rs61141967	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62572968	0.80[EUR][1000 genomes]
rs62572970	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62572971	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62572990	0.95[ASN][1000 genomes]
rs6474906	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7036966	0.83[ASN][1000 genomes]
rs72702776	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7855551	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7870605	0.88[CHB][hapmap];0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7870630	0.88[CHB][hapmap];0.92[YRI][hapmap];0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][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:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:15349000-15357600	Enhancers	HepG2	liver
2	chr9:15351600-15357200	Weak transcription	Thymus	Thymus
3	chr9:15353600-15357400	Enhancers	Primary hematopoietic stem cells short term culture	blood
4	chr9:15354000-15357600	Enhancers	Primary T cells from cord blood	blood
5	chr9:15354600-15357600	Enhancers	Primary hematopoietic stem cells	blood
6	chr9:15355200-15358400	Enhancers	Fetal Intestine Small	intestine
7	chr9:15355400-15358600	Enhancers	Fetal Intestine Large	intestine
8	chr9:15355600-15357200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
9	chr9:15356000-15357000	Weak transcription	Fetal Thymus	thymus
10	chr9:15356000-15357200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr9:15356000-15357200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr9:15356000-15357200	Weak transcription	Primary T cells fromperipheralblood	blood
13	chr9:15356200-15357000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
14	chr9:15356200-15357200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
15	chr9:15356200-15362800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr9:15356400-15358000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr9:15356600-15357200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr9:15356600-15357400	Enhancers	HUES48 Cell Line	embryonic stem cell
19	chr9:15356600-15357400	Enhancers	Primary T helper cells fromperipheralblood	blood
20	chr9:15356600-15357600	Enhancers	Primary T helper cells PMA-I stimulated	--
21	chr9:15356800-15357000	Enhancers	HUES6 Cell Line	embryonic stem cell
22	chr9:15356800-15357400	Enhancers	HUES64 Cell Line	embryonic stem cell
23	chr9:15356800-15357600	Enhancers	iPS-15b Cell Line	embryonic stem cell
24	chr9:15356800-15357600	Enhancers	Rectal Mucosa Donor 31	rectum
25	chr9:15356800-15358000	Enhancers	Rectal Mucosa Donor 29	rectum

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