Variant report

Variant	rs1413178
Chromosome Location	chr9:98586312-98586313
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:98583596..98587083-chr9:98587311..98591492,4	MCF-7	breast:
2	chr9:98585623..98589276-chr9:98636803..98639212,4	MCF-7	breast:
3	chr9:98569719..98571881-chr9:98585000..98587559,2	MCF-7	breast:
4	chr9:98571797..98574683-chr9:98583300..98586661,3	MCF-7	breast:
5	chr9:98584113..98586604-chr9:98610986..98613982,2	MCF-7	breast:
6	chr9:98578285..98580022-chr9:98583507..98586457,2	MCF-7	breast:
7	chr9:98585752..98588064-chr9:98594275..98596472,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000175611	Chromatin interaction
ENSG00000182150	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs12003772	0.88[ASN][1000 genomes]
rs12551596	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12551880	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12554182	1.00[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12555687	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16910333	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs16910342	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs16910409	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs16910427	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs17303073	0.88[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17303324	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2280143	0.89[JPT][hapmap]
rs2297009	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs2423	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs3739755	0.95[ASN][1000 genomes]
rs3739756	1.00[CHB][hapmap];0.95[CHD][hapmap];0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs4742763	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4742769	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4742801	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs4743327	0.82[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4743351	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4743383	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs4743460	0.88[ASN][1000 genomes]
rs4743469	0.81[ASN][1000 genomes]
rs55651016	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs55770584	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs55781050	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55797980	0.88[ASN][1000 genomes]
rs55881510	0.91[ASN][1000 genomes]
rs56063686	0.95[ASN][1000 genomes]
rs56070531	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56110216	0.91[ASN][1000 genomes]
rs56125887	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56372801	0.88[ASN][1000 genomes]
rs56403401	0.91[ASN][1000 genomes]
rs57096664	0.97[ASN][1000 genomes]
rs59046245	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59189545	0.95[ASN][1000 genomes]
rs61036807	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61093440	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9721742	0.95[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9792431	0.88[ASN][1000 genomes]
rs9792684	1.00[CHB][hapmap];0.90[JPT][hapmap];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv893598	chr9:98508628-98645674	Weak transcription Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
2	nsv482884	chr9:98530027-98691937	Weak transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Strong transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
3	nsv893599	chr9:98542410-98991254	Bivalent Enhancer Enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	52 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	chr9:98570400-98589200	Weak transcription	Left Ventricle	heart
2	chr9:98570400-98589200	Weak transcription	Right Ventricle	heart
3	chr9:98570400-98593200	Weak transcription	Gastric	stomach
4	chr9:98570400-98593800	Weak transcription	Right Atrium	heart
5	chr9:98570800-98601400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr9:98576000-98596000	Weak transcription	Aorta	Aorta
7	chr9:98581800-98593800	Weak transcription	Fetal Intestine Small	intestine
8	chr9:98583800-98586600	Enhancers	Placenta Amnion	Placenta Amnion
9	chr9:98585200-98593600	Weak transcription	Spleen	Spleen
10	chr9:98585800-98588200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr9:98585800-98588800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr9:98585800-98589200	Weak transcription	Lung	lung
13	chr9:98585800-98592200	Weak transcription	Ovary	ovary
14	chr9:98585800-98593200	Weak transcription	Fetal Stomach	stomach
15	chr9:98585800-98593200	Weak transcription	Stomach Smooth Muscle	stomach
16	chr9:98586000-98586400	Enhancers	Hela-S3	cervix
17	chr9:98586000-98586600	Enhancers	GM12878-XiMat	blood
18	chr9:98586000-98587600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr9:98586000-98588200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
20	chr9:98586000-98588600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr9:98586000-98593200	Weak transcription	Rectal Mucosa Donor 31	rectum
22	chr9:98586200-98588200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr9:98586200-98588200	Weak transcription	HUVEC	blood vessel

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