Variant report

Variant	rs13290518
Chromosome Location	chr9:101066578-101066579
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:101063724..101066732-chr9:101068863..101071288,3	MCF-7	breast:
2	chr9:101064801..101068003-chr9:101068500..101071680,4	K562	blood:
3	chr9:100684379..100686017-chr9:101064394..101066940,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000136932	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10985791	0.89[JPT][hapmap];0.80[ASN][1000 genomes]
rs10985795	1.00[ASW][hapmap];0.87[CEU][hapmap];0.86[CHB][hapmap];0.91[GIH][hapmap];0.82[JPT][hapmap];1.00[LWK][hapmap];0.97[TSI][hapmap];0.95[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10985799	0.94[CHB][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10985800	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10985811	0.81[ASW][hapmap];0.90[CHB][hapmap];0.84[LWK][hapmap];0.95[YRI][hapmap];0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs13286336	0.87[CEU][hapmap];0.90[YRI][hapmap];0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13300613	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1415111	0.87[CHB][hapmap];0.84[JPT][hapmap];0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2304390	0.81[LWK][hapmap]
rs34283833	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs35126377	0.90[EUR][1000 genomes]
rs3780440	0.91[EUR][1000 genomes]
rs3780441	0.86[CEU][hapmap];0.88[GIH][hapmap];0.81[JPT][hapmap];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3780442	0.87[CEU][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3780443	0.81[ASW][hapmap];0.81[CEU][hapmap];0.95[GIH][hapmap];0.92[LWK][hapmap];0.89[TSI][hapmap];0.95[YRI][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3780446	0.87[GIH][hapmap]
rs56220486	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7022133	0.90[EUR][1000 genomes]
rs7850445	0.84[JPT][hapmap];0.84[ASN][1000 genomes]
rs7875521	0.89[JPT][hapmap]
rs970388	0.89[JPT][hapmap];0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv430085	chr9:100928245-101339645	Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
2	nsv831663	chr9:100941048-101109492	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
3	nsv1045780	chr9:100943318-101080389	Flanking Bivalent TSS/Enh Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
4	nsv540180	chr9:100943318-101080389	Enhancers Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
5	nsv831664	chr9:101024862-101205637	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	nsv519818	chr9:101024887-101092316	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats	Chromatin interactive region	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:101055400-101068400	Weak transcription	Brain Germinal Matrix	brain
2	chr9:101061400-101067200	Weak transcription	Brain Cingulate Gyrus	brain
3	chr9:101061600-101083400	Weak transcription	Brain Angular Gyrus	brain
4	chr9:101061800-101070000	Enhancers	Placenta	Placenta
5	chr9:101062000-101078000	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr9:101063400-101071600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr9:101063600-101071800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr9:101063800-101068000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr9:101064600-101067000	Strong transcription	Fetal Brain Female	brain
10	chr9:101064600-101067000	Enhancers	Fetal Muscle Trunk	muscle
11	chr9:101064600-101069000	Weak transcription	HUVEC	blood vessel
12	chr9:101064800-101067000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr9:101065400-101067000	Enhancers	Fetal Muscle Leg	muscle
14	chr9:101065800-101066600	Enhancers	H1 Cell Line	embryonic stem cell
15	chr9:101065800-101067000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr9:101066000-101067000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr9:101066000-101072000	Weak transcription	Cortex derived primary cultured neurospheres	brain
18	chr9:101066200-101068800	Weak transcription	K562	blood
19	chr9:101066400-101066600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr9:101066400-101066600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr9:101066400-101066800	Enhancers	HUES6 Cell Line	embryonic stem cell

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