Variant report

Variant	rs55875249
Chromosome Location	chr4:87642948-87642949
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	chr4:87592727..87594779-chr4:87641743..87643865,2	MCF-7	breast:

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs10516779	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10516781	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17012014	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17012069	1.00[AMR][1000 genomes]
rs61537748	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61734716	1.00[AMR][1000 genomes]
rs73835705	1.00[AMR][1000 genomes]
rs73835706	1.00[AMR][1000 genomes]
rs73835709	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73835713	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73835762	1.00[AMR][1000 genomes]
rs73835765	1.00[AMR][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	nsv594787	chr4:87221827-87888667	Enhancers Weak transcription Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
2	nsv1012836	chr4:87279206-87643558	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
3	esv2757071	chr4:87417291-87689533	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
4	esv2759264	chr4:87417291-87689533	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
5	nsv879522	chr4:87473776-87644842	Weak transcription ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv830001	chr4:87585278-87748643	Enhancers Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases
7	nsv508296	chr4:87636350-87667372	ZNF genes & repeats Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:87574600-87644400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
2	chr4:87579400-87644400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr4:87586400-87643200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
4	chr4:87592400-87656400	Weak transcription	Adipose Nuclei	Adipose
5	chr4:87594400-87659800	Weak transcription	Ovary	ovary
6	chr4:87595200-87651200	Weak transcription	Fetal Stomach	stomach
7	chr4:87623400-87643000	Weak transcription	Fetal Lung	lung
8	chr4:87625200-87651600	Weak transcription	Esophagus	oesophagus
9	chr4:87625400-87643400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr4:87631200-87712200	Weak transcription	Aorta	Aorta
11	chr4:87635200-87737400	Weak transcription	Fetal Brain Male	brain
12	chr4:87635400-87648200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr4:87635600-87651600	Weak transcription	Lung	lung
14	chr4:87636400-87644600	Weak transcription	Fetal Intestine Small	intestine
15	chr4:87636400-87683800	Weak transcription	Stomach Smooth Muscle	stomach
16	chr4:87636800-87643400	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr4:87637200-87661200	Weak transcription	Pancreas	Pancrea
18	chr4:87638600-87643600	Strong transcription	HUES64 Cell Line	embryonic stem cell
19	chr4:87638600-87644400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr4:87639000-87643000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr4:87639200-87688000	Weak transcription	Fetal Intestine Large	intestine
22	chr4:87639400-87739200	Weak transcription	A549	lung
23	chr4:87639600-87643200	Weak transcription	Fetal Kidney	kidney
24	chr4:87639600-87644400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr4:87639600-87644400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
26	chr4:87639800-87643200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
27	chr4:87640200-87643200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr4:87640200-87652000	Weak transcription	HMEC	breast
29	chr4:87640400-87643000	Weak transcription	H1 Cell Line	embryonic stem cell
30	chr4:87640400-87643000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
31	chr4:87640600-87643200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr4:87641600-87643000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr4:87641600-87643400	Strong transcription	HUES48 Cell Line	embryonic stem cell
34	chr4:87641600-87660400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
35	chr4:87641800-87648400	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr4:87641800-87683400	Weak transcription	Duodenum Smooth Muscle	Duodenum
37	chr4:87642000-87644200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr4:87642000-87644400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr4:87642000-87644400	Weak transcription	NHEK	skin
40	chr4:87642000-87651200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
41	chr4:87642000-87651600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
42	chr4:87642000-87651600	Weak transcription	Gastric	stomach
43	chr4:87642000-87655200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
44	chr4:87642000-87661000	Weak transcription	Brain Inferior Temporal Lobe	brain
45	chr4:87642200-87643200	Weak transcription	NHLF	lung
46	chr4:87642200-87643400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr4:87642200-87692600	Weak transcription	NH-A	brain
48	chr4:87642400-87643000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr4:87642400-87643200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr4:87642400-87643200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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