Variant report

Variant	rs2070616
Chromosome Location	chr3:53755961-53755962
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:53754923..53757308-chr3:53878657..53881028,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000016391	Chromatin interaction
ENSG00000056736	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs1020822	0.93[ASN][1000 genomes]
rs11130380	0.90[ASN][1000 genomes]
rs11708934	0.93[ASN][1000 genomes]
rs17053382	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17053417	0.90[ASN][1000 genomes]
rs17053459	0.83[ASN][1000 genomes]
rs2029331	0.91[ASN][1000 genomes]
rs2248381	0.87[ASN][1000 genomes]
rs2306865	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2306866	0.84[ASN][1000 genomes]
rs2633723	0.95[ASN][1000 genomes]
rs3796346	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62253777	0.92[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62253778	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6800641	0.93[ASN][1000 genomes]
rs723540	0.93[ASN][1000 genomes]
rs7628839	0.88[ASN][1000 genomes]
rs898423	0.91[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	nsv1003621	chr3:53448934-54425322	Active TSS Strong transcription Bivalent Enhancer Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv1001128	chr3:53659570-53927842	Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	nsv1013783	chr3:53694418-53934781	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
4	nsv1007655	chr3:53742148-53767689	Active TSS Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
5	nsv1002452	chr3:53742148-53802811	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
6	nsv1000280	chr3:53742736-53770588	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats	Chromatin interactive region	3 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	chr3:53740200-53764400	Weak transcription	Brain Cingulate Gyrus	brain
2	chr3:53742600-53778000	Weak transcription	Pancreas	Pancrea
3	chr3:53744200-53764600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr3:53744400-53756600	Weak transcription	Lung	lung
5	chr3:53744400-53758600	Weak transcription	Stomach Smooth Muscle	stomach
6	chr3:53744400-53763800	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr3:53744600-53756400	Weak transcription	Liver	Liver
8	chr3:53744600-53761200	Weak transcription	Duodenum Mucosa	Duodenum
9	chr3:53745200-53762800	Strong transcription	Fetal Intestine Large	intestine
10	chr3:53748600-53756200	Weak transcription	Fetal Brain Male	brain
11	chr3:53752400-53756400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
12	chr3:53752400-53756600	Weak transcription	Fetal Lung	lung
13	chr3:53753200-53761000	Weak transcription	Spleen	Spleen
14	chr3:53753400-53760800	Weak transcription	Duodenum Smooth Muscle	Duodenum
15	chr3:53753600-53766200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr3:53753800-53756200	Enhancers	Pancreatic Islets	Pancreatic Islet
17	chr3:53754200-53763600	Weak transcription	Brain Hippocampus Middle	brain
18	chr3:53754600-53756200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr3:53755000-53756000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr3:53755000-53756000	Enhancers	NHDF-Ad	bronchial
21	chr3:53755200-53761600	Strong transcription	Fetal Intestine Small	intestine
22	chr3:53755200-53764400	Weak transcription	Brain Angular Gyrus	brain
23	chr3:53755600-53757400	Weak transcription	Brain Inferior Temporal Lobe	brain
24	chr3:53755600-53764400	Weak transcription	Brain Anterior Caudate	brain
25	chr3:53755800-53756000	Enhancers	H9 Cell Line	embryonic stem cell

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