Variant report

Variant	rs55684110
Chromosome Location	chr1:209541832-209541833
allele	A/T
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	GATA3	chr1:209541476-209541992	SK-N-SH	brain:	n/a	n/a
2	GATA3	chr1:209541559-209541879	T-47D	breast:	n/a	n/a
3	GATA3	chr1:209541337-209543157	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:209532175..209545038-chr1:209598052..209610156,35	MCF-7	breast:
2	chr1:209541024..209542920-chr1:209555785..209557291,2	MCF-7	breast:
3	chr1:209399241..209400998-chr1:209541638..209543398,2	MCF-7	breast:
4	chr1:209527253..209544360-chr1:209599669..209610889,45	MCF-7	breast:

Variant related genes	Relation type
ENSG00000231648	TF binding region
ENSG00000230937	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs1006316	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1006317	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10494921	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1354850	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1354852	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1354853	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1395753	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1507331	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1507336	0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17014320	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17014323	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17014337	0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17014370	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17014375	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17014395	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17014396	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4844473	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4844807	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4844809	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4844815	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4844820	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4844821	0.97[ASN][1000 genomes]
rs58017268	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60460414	0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs60534728	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6674793	0.83[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs6681466	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs74155473	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7516757	0.81[ASN][1000 genomes]
rs7516864	0.84[ASN][1000 genomes]
rs7548184	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832492	chr1:209383771-209589312	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	esv3496690	chr1:209541075-209543370	Enhancers Weak transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	esv3496691	chr1:209541075-209543370	Enhancers Weak transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:209526400-209545600	Enhancers	Breast Myoepithelial Primary Cells	Breast
2	chr1:209529800-209547000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr1:209535400-209543800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr1:209535800-209542200	Enhancers	NHEK	skin
5	chr1:209535800-209550800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr1:209536000-209545200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr1:209536000-209545600	Enhancers	HMEC	breast
8	chr1:209536800-209548600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr1:209537600-209548600	Weak transcription	HUES48 Cell Line	embryonic stem cell
10	chr1:209538000-209543200	Weak transcription	Fetal Thymus	thymus
11	chr1:209538000-209547200	Weak transcription	HUES6 Cell Line	embryonic stem cell
12	chr1:209538600-209542200	Weak transcription	HSMMtube	muscle
13	chr1:209539800-209543200	Enhancers	NH-A	brain
14	chr1:209539800-209545600	Enhancers	Fetal Brain Male	brain
15	chr1:209540000-209542400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr1:209540000-209542400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr1:209540000-209542800	Enhancers	Placenta Amnion	Placenta Amnion
18	chr1:209540000-209542800	Enhancers	HSMM	muscle
19	chr1:209540200-209542400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr1:209540200-209543000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr1:209540200-209543200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr1:209540200-209543400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr1:209540200-209544600	Enhancers	Fetal Brain Female	brain
24	chr1:209540400-209543000	Enhancers	Fetal Muscle Leg	muscle
25	chr1:209540400-209549200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
26	chr1:209540600-209542200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
27	chr1:209540600-209546200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
28	chr1:209540800-209542200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr1:209540800-209542200	Weak transcription	Fetal Stomach	stomach
30	chr1:209540800-209542400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr1:209540800-209542400	Enhancers	Muscle Satellite Cultured Cells	--
32	chr1:209541200-209542200	Enhancers	Osteobl	bone
33	chr1:209541200-209548600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr1:209541600-209542400	Enhancers	Hela-S3	cervix
35	chr1:209541800-209542200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr1:209541800-209542200	Weak transcription	Esophagus	oesophagus
37	chr1:209541800-209543200	Enhancers	NHLF	lung

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