Variant report

Variant	rs55643410
Chromosome Location	chr4:104008420-104008421
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr4:104008348-104008563	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr4:103789095..103791154-chr4:104008357..104010785,2	MCF-7	breast:
2	chr4:104000908..104002877-chr4:104007976..104009657,2	K562	blood:
3	chr4:104007330..104009094-chr4:104010936..104013359,2	K562	blood:
4	chr4:104005166..104007100-chr4:104007748..104010195,2	K562	blood:

Variant related genes	Relation type
SLC9B2	TF binding region
ENSG00000109332	Chromatin interaction
ENSG00000164038	Chromatin interaction
ENSG00000145354	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs6831995	1.00[AMR][1000 genomes]
rs6834690	1.00[AMR][1000 genomes]
rs6851455	1.00[AMR][1000 genomes]
rs72937427	1.00[AMR][1000 genomes]
rs72937428	1.00[AMR][1000 genomes]
rs72937431	1.00[AMR][1000 genomes]
rs72937478	1.00[AMR][1000 genomes]
rs9684904	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2757946	chr4:103780705-104057321	Strong transcription Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	esv2759270	chr4:103780705-104057321	ZNF genes & repeats Strong transcription Weak transcription Active TSS Bivalent Enhancer Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
3	esv3429917	chr4:103915319-104207455	ZNF genes & repeats Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
4	nsv830021	chr4:103934454-104100588	Active TSS Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:103998200-104010000	Weak transcription	Small Intestine	intestine
2	chr4:103998200-104011200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr4:103998200-104020400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr4:103998400-104010800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr4:103998400-104018800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr4:103998600-104009600	Weak transcription	Primary B cells from peripheral blood	blood
7	chr4:103998600-104011200	Weak transcription	Brain Cingulate Gyrus	brain
8	chr4:103998600-104011600	Weak transcription	NHDF-Ad	bronchial
9	chr4:103998600-104020200	Weak transcription	Fetal Brain Male	brain
10	chr4:103998800-104009600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr4:103998800-104013400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
12	chr4:103998800-104019600	Weak transcription	NHEK	skin
13	chr4:103999000-104009800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr4:103999000-104010600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
15	chr4:103999000-104020200	Weak transcription	Hela-S3	cervix
16	chr4:103999400-104013600	Weak transcription	Primary neutrophils fromperipheralblood	blood
17	chr4:104000000-104012400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
18	chr4:104000200-104016400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr4:104000400-104012400	Strong transcription	Duodenum Mucosa	Duodenum
20	chr4:104000400-104014600	Strong transcription	Fetal Intestine Large	intestine
21	chr4:104000600-104016400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr4:104000800-104012800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr4:104000800-104013000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr4:104000800-104013600	Strong transcription	Primary T cells from cord blood	blood
25	chr4:104001000-104012400	Strong transcription	Liver	Liver
26	chr4:104001600-104013800	Strong transcription	HUES64 Cell Line	embryonic stem cell
27	chr4:104001800-104012400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr4:104001800-104015000	Strong transcription	Fetal Lung	lung
29	chr4:104002000-104012800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr4:104003200-104013200	Strong transcription	HSMM	muscle
31	chr4:104003800-104011200	Weak transcription	Fetal Heart	heart
32	chr4:104005000-104013600	Strong transcription	Fetal Muscle Trunk	muscle
33	chr4:104005000-104014000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr4:104005200-104013000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
35	chr4:104005200-104013400	Strong transcription	Adipose Nuclei	Adipose
36	chr4:104005400-104012200	Strong transcription	Rectal Mucosa Donor 29	rectum
37	chr4:104005400-104012400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr4:104005400-104012400	Strong transcription	Stomach Smooth Muscle	stomach
39	chr4:104005400-104012600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr4:104005400-104012600	Strong transcription	Ovary	ovary
41	chr4:104005400-104012600	Strong transcription	Dnd41	blood
42	chr4:104005400-104014800	Strong transcription	Fetal Muscle Leg	muscle
43	chr4:104005400-104015600	Strong transcription	Skeletal Muscle Female	skeletal muscle
44	chr4:104005400-104016400	Strong transcription	Fetal Thymus	thymus
45	chr4:104005600-104012400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr4:104005600-104012400	Strong transcription	Cortex derived primary cultured neurospheres	brain
47	chr4:104005800-104008800	Strong transcription	HSMMtube	muscle
48	chr4:104006000-104012400	Strong transcription	Duodenum Smooth Muscle	Duodenum
49	chr4:104006000-104012600	Strong transcription	Primary hematopoietic stem cells	blood
50	chr4:104006200-104012400	Strong transcription	iPS-18 Cell Line	embryonic stem cell

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