Variant report

Variant	rs9789479
Chromosome Location	chr2:47543245-47543246
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:47542272..47544108-chr2:47546260..47549023,2	MCF-7	breast:
2	chr2:47395267..47408439-chr2:47533772..47553038,55	MCF-7	breast:
3	chr2:47418771..47421369-chr2:47540546..47543662,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000143933	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs10168995	1.00[GIH][hapmap]
rs10180711	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12471906	0.91[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4558636	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4560164	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6544977	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6544978	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6720211	0.82[CHB][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9789683	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv817517	chr2:46819371-47715140	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
2	nsv1004828	chr2:47056849-47814482	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	144 gene(s)	inside rSNPs	diseases
3	nsv531348	chr2:47433147-47827310	Flanking Bivalent TSS/Enh Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer 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	50 gene(s)	inside rSNPs	diseases
4	nsv457385	chr2:47468331-47552277	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv581755	chr2:47468331-47552277	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Strong transcription	Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	nsv999576	chr2:47506116-47773960	Weak transcription Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
7	nsv524003	chr2:47543245-47590034	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:47534400-47550400	Weak transcription	Ovary	ovary
2	chr2:47538400-47550200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr2:47538400-47552600	Weak transcription	Fetal Brain Female	brain
4	chr2:47538600-47548400	Weak transcription	Fetal Stomach	stomach
5	chr2:47538600-47548800	Weak transcription	NH-A	brain
6	chr2:47538600-47550200	Weak transcription	Fetal Lung	lung
7	chr2:47538800-47550400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr2:47538800-47550600	Weak transcription	Lung	lung
9	chr2:47539000-47548800	Weak transcription	Cortex derived primary cultured neurospheres	brain
10	chr2:47539000-47550200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr2:47540600-47546800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr2:47540600-47548600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr2:47541000-47546800	Weak transcription	Brain Angular Gyrus	brain
14	chr2:47541000-47546800	Weak transcription	Brain Anterior Caudate	brain
15	chr2:47541000-47546800	Weak transcription	Brain Cingulate Gyrus	brain
16	chr2:47541000-47548200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr2:47541000-47548600	Weak transcription	HUES6 Cell Line	embryonic stem cell
18	chr2:47541000-47550200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr2:47541200-47546800	Weak transcription	Brain Hippocampus Middle	brain
20	chr2:47541400-47546400	Weak transcription	Brain Inferior Temporal Lobe	brain
21	chr2:47541400-47546800	Weak transcription	Brain Substantia Nigra	brain
22	chr2:47541400-47547000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr2:47541400-47550000	Weak transcription	Adipose Nuclei	Adipose
24	chr2:47542000-47543600	Enhancers	Fetal Intestine Large	intestine
25	chr2:47542400-47543600	Enhancers	Rectal Mucosa Donor 31	rectum
26	chr2:47542400-47543600	Enhancers	Stomach Mucosa	stomach
27	chr2:47542400-47543600	Enhancers	HepG2	liver
28	chr2:47542600-47543400	Enhancers	A549	lung
29	chr2:47542800-47548000	Weak transcription	Duodenum Mucosa	Duodenum
30	chr2:47543000-47543600	ZNF genes & repeats	Fetal Intestine Small	intestine
31	chr2:47543000-47550000	Weak transcription	Colonic Mucosa	Colon
32	chr2:47543200-47543400	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr2:47543200-47563400	Weak transcription	Sigmoid Colon	Sigmoid Colon

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