Variant report

Variant	rs62250930
Chromosome Location	chr3:53851245-53851246
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	chr3:53849527..53851449-chr3:53878802..53881652,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000056736	Chromatin interaction
ENSG00000016391	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs10154841	0.80[ASN][1000 genomes]
rs10490844	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62250902	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62250931	0.91[ASN][1000 genomes]
rs9836592	0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 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

No data

Chromatin state (count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:53829200-53853000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr3:53839200-53855200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr3:53839400-53851400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
4	chr3:53839600-53852800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
5	chr3:53839600-53876600	Weak transcription	HUES64 Cell Line	embryonic stem cell
6	chr3:53840800-53853600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
7	chr3:53841000-53852600	Weak transcription	Ovary	ovary
8	chr3:53841000-53852800	Weak transcription	Stomach Smooth Muscle	stomach
9	chr3:53841600-53851400	Weak transcription	Fetal Muscle Leg	muscle
10	chr3:53841600-53851400	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr3:53841600-53855600	Weak transcription	Right Ventricle	heart
12	chr3:53841600-53855800	Weak transcription	Right Atrium	heart
13	chr3:53841800-53853400	Weak transcription	Fetal Brain Female	brain
14	chr3:53841800-53853400	Weak transcription	GM12878-XiMat	blood
15	chr3:53842200-53852200	Strong transcription	Fetal Intestine Small	intestine
16	chr3:53842200-53852600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr3:53842200-53857200	Strong transcription	Fetal Intestine Large	intestine
18	chr3:53842400-53855600	Weak transcription	Fetal Heart	heart
19	chr3:53844400-53852000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr3:53846600-53879800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr3:53847000-53856400	Weak transcription	Brain Germinal Matrix	brain
22	chr3:53847000-53862000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr3:53847600-53852200	Weak transcription	Skeletal Muscle Female	skeletal muscle
24	chr3:53848200-53851800	Weak transcription	Esophagus	oesophagus
25	chr3:53849000-53857200	Strong transcription	Duodenum Mucosa	Duodenum
26	chr3:53849000-53857800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr3:53849000-53858200	Strong transcription	Fetal Stomach	stomach
28	chr3:53849000-53858800	Strong transcription	Liver	Liver
29	chr3:53849000-53859200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
30	chr3:53849000-53866800	Weak transcription	Stomach Mucosa	stomach
31	chr3:53849200-53852000	Enhancers	Cortex derived primary cultured neurospheres	brain
32	chr3:53849200-53853800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr3:53849400-53851600	Weak transcription	Primary neutrophils fromperipheralblood	blood
34	chr3:53849400-53851600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr3:53849600-53851400	Weak transcription	H9 Cell Line	embryonic stem cell
36	chr3:53849600-53875400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr3:53849800-53851600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
38	chr3:53850000-53851600	Weak transcription	Brain Cingulate Gyrus	brain
39	chr3:53850000-53855200	Strong transcription	Brain Inferior Temporal Lobe	brain
40	chr3:53850200-53851800	Weak transcription	Skeletal Muscle Male	skeletal muscle
41	chr3:53850600-53851600	Weak transcription	Fetal Muscle Trunk	muscle
42	chr3:53850600-53851600	Strong transcription	HepG2	liver
43	chr3:53850600-53857400	Strong transcription	Rectal Mucosa Donor 29	rectum
44	chr3:53850800-53851400	Weak transcription	Brain Hippocampus Middle	brain
45	chr3:53850800-53851800	Genic enhancers	Brain Anterior Caudate	brain
46	chr3:53850800-53854600	Strong transcription	Pancreatic Islets	Pancreatic Islet
47	chr3:53850800-53858600	Strong transcription	Gastric	stomach
48	chr3:53851000-53851800	Genic enhancers	Brain Angular Gyrus	brain
49	chr3:53851000-53852200	Genic enhancers	Brain Dorsolateral Prefrontal Cortex	brain
50	chr3:53851000-53854400	Strong transcription	HUES6 Cell Line	embryonic stem cell

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