Variant report

Variant	rs61746180
Chromosome Location	chr3:53857982-53857983
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:53857432..53859908-chr3:53878977..53881329,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000016391	Chromatin interaction
ENSG00000056736	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:1)

rs_ID	r²[population]
rs6775991	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 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	nsv1003204	chr3:53820070-53877149	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv1002375	chr3:53822319-53872753	Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	nsv876803	chr3:53822893-53889849	Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
7	nsv518466	chr3:53832903-53882663	Weak transcription Enhancers Bivalent/Poised TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
8	nsv521181	chr3:53833509-53881471	Weak transcription Strong transcription Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
9	nsv876804	chr3:53833509-53934171	Flanking Active TSS Weak transcription Strong transcription Genic enhancers Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
10	nsv1010575	chr3:53846741-53934781	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
11	nsv1006990	chr3:53849510-54285212	Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
12	nsv997771	chr3:53852695-53926635	Enhancers Bivalent/Poised TSS Active TSS Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:53839600-53876600	Weak transcription	HUES64 Cell Line	embryonic stem cell
2	chr3:53846600-53879800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr3:53847000-53862000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr3:53849000-53858200	Strong transcription	Fetal Stomach	stomach
5	chr3:53849000-53858800	Strong transcription	Liver	Liver
6	chr3:53849000-53859200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
7	chr3:53849000-53866800	Weak transcription	Stomach Mucosa	stomach
8	chr3:53849600-53875400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr3:53850800-53858600	Strong transcription	Gastric	stomach
10	chr3:53851000-53858000	Strong transcription	Pancreas	Pancrea
11	chr3:53851200-53858000	Strong transcription	H1 Cell Line	embryonic stem cell
12	chr3:53851600-53858000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr3:53852400-53865000	Weak transcription	Aorta	Aorta
14	chr3:53852400-53878200	Weak transcription	Hela-S3	cervix
15	chr3:53853000-53858200	Strong transcription	Fetal Intestine Small	intestine
16	chr3:53853000-53858800	Strong transcription	Cortex derived primary cultured neurospheres	brain
17	chr3:53853200-53867400	Weak transcription	Lung	lung
18	chr3:53853400-53858200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr3:53853400-53877200	Weak transcription	Colonic Mucosa	Colon
20	chr3:53853600-53861800	Weak transcription	Primary neutrophils fromperipheralblood	blood
21	chr3:53853600-53866800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr3:53853800-53879000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr3:53854000-53879400	Weak transcription	H9 Cell Line	embryonic stem cell
24	chr3:53854200-53871600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr3:53854200-53877400	Weak transcription	Esophagus	oesophagus
26	chr3:53854400-53858000	Weak transcription	HUES6 Cell Line	embryonic stem cell
27	chr3:53854400-53873000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
28	chr3:53854400-53876400	Weak transcription	Sigmoid Colon	Sigmoid Colon
29	chr3:53854600-53858000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
30	chr3:53854600-53859600	Weak transcription	Pancreatic Islets	Pancreatic Islet
31	chr3:53854600-53862600	Weak transcription	Brain Anterior Caudate	brain
32	chr3:53854600-53866600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr3:53854600-53867400	Weak transcription	Spleen	Spleen
34	chr3:53854600-53873200	Weak transcription	HUES48 Cell Line	embryonic stem cell
35	chr3:53855800-53862000	Weak transcription	Brain Substantia Nigra	brain
36	chr3:53856000-53858800	Strong transcription	HepG2	liver
37	chr3:53856200-53859000	Weak transcription	Skeletal Muscle Male	skeletal muscle
38	chr3:53856200-53866000	Weak transcription	Brain Cingulate Gyrus	brain
39	chr3:53856600-53862200	Weak transcription	Brain Hippocampus Middle	brain
40	chr3:53856800-53879200	Weak transcription	Ovary	ovary
41	chr3:53857000-53862600	Weak transcription	Brain Inferior Temporal Lobe	brain
42	chr3:53857200-53858400	Weak transcription	Fetal Intestine Large	intestine
43	chr3:53857200-53863000	Weak transcription	Duodenum Mucosa	Duodenum
44	chr3:53857400-53858200	Weak transcription	Rectal Mucosa Donor 31	rectum
45	chr3:53857400-53876400	Weak transcription	Rectal Mucosa Donor 29	rectum
46	chr3:53857400-53876800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
47	chr3:53857800-53858600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
48	chr3:53857800-53858800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr3:53857800-53865000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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