Variant report

Variant	rs55840318
Chromosome Location	chr3:50527914-50527915
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:50526587..50528932-chr3:50530037..50531864,2	MCF-7	breast:
2	chr3:50526765..50528739-chr3:50533687..50536379,2	MCF-7	breast:
3	chr3:50525621..50528608-chr3:50539997..50541654,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000007402	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs4560294	1.00[EUR][1000 genomes]
rs73835510	1.00[EUR][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	nsv523662	chr3:50144951-50584999	Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	101 gene(s)	inside rSNPs	diseases
2	esv1821728	chr3:50156142-50657253	Strong transcription Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	109 gene(s)	inside rSNPs	diseases
3	nsv470561	chr3:50158774-50584999	Flanking Active TSS Enhancers Weak transcription Genic enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	99 gene(s)	inside rSNPs	diseases
4	nsv876770	chr3:50158774-50609624	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
5	nsv1001993	chr3:50187646-50640808	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
6	esv3584502	chr3:50368278-50659741	Strong transcription Bivalent/Poised TSS Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
7	nsv432419	chr3:50388396-50637496	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
8	nsv1013225	chr3:50440826-50700448	Flanking Active TSS Enhancers Genic enhancers Weak transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
9	nsv536566	chr3:50440826-50700448	Genic enhancers Weak transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
10	nsv984540	chr3:50473691-50669310	Enhancers Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
11	nsv1012501	chr3:50483037-50679591	Bivalent Enhancer Flanking Active TSS Enhancers Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
12	nsv536567	chr3:50483037-50679591	Bivalent Enhancer Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS 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	27 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:50492600-50528400	Weak transcription	Gastric	stomach
2	chr3:50520400-50530400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
3	chr3:50520800-50528400	Weak transcription	Spleen	Spleen
4	chr3:50522000-50533600	Weak transcription	Lung	lung
5	chr3:50522800-50528000	Weak transcription	HUES6 Cell Line	embryonic stem cell
6	chr3:50525000-50528200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
7	chr3:50525400-50528000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr3:50525400-50528000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr3:50525600-50528000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr3:50525800-50528000	Weak transcription	H1 Cell Line	embryonic stem cell
11	chr3:50525800-50528000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
12	chr3:50527200-50529200	Enhancers	Fetal Muscle Leg	muscle
13	chr3:50527200-50529400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
14	chr3:50527400-50529200	Enhancers	Primary hematopoietic stem cells short term culture	blood
15	chr3:50527400-50529400	Bivalent Enhancer	Fetal Muscle Trunk	muscle
16	chr3:50527400-50529800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr3:50527600-50528000	Weak transcription	Right Atrium	heart
18	chr3:50527600-50529400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr3:50527600-50529600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr3:50527600-50530000	Enhancers	Right Ventricle	heart
21	chr3:50527800-50528200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr3:50527800-50528200	Enhancers	Fetal Kidney	kidney
23	chr3:50527800-50528400	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
24	chr3:50527800-50528800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr3:50527800-50529400	Enhancers	Primary hematopoietic stem cells	blood
26	chr3:50527800-50529600	Enhancers	Fetal Thymus	thymus
27	chr3:50527800-50529800	Enhancers	Left Ventricle	heart

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