Variant report

Variant	rs7543927
Chromosome Location	chr1:180953038-180953039
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:180940787..180943188-chr1:180951755..180953888,2	MCF-7	breast:
2	chr1:180943968..180947141-chr1:180950568..180953802,3	MCF-7	breast:
3	chr1:180951063..180953741-chr1:181057832..181059498,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000243155	Chromatin interaction
ENSG00000234237	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs1044595	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10753232	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11586493	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12744212	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12754041	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1411478	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2331903	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3747957	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3789362	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3789364	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4111520	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4495657	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4652545	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4652547	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4652548	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs59145927	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6425657	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6425658	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6665134	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6680541	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7516739	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7528526	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7553330	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[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	nsv1014404	chr1:180770155-181090200	Weak transcription Active TSS Enhancers Genic enhancers Strong transcription Flanking Active TSS 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	97 gene(s)	inside rSNPs	diseases
2	esv3342865	chr1:180933678-181018012	Flanking Active TSS Strong transcription Weak transcription Enhancers Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
3	esv3383831	chr1:180937224-181029755	Strong transcription Active TSS Weak transcription Genic enhancers Flanking Active TSS Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:180923600-180958800	Weak transcription	Small Intestine	intestine
2	chr1:180929000-180956200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr1:180933400-180974600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr1:180939200-180954400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr1:180939200-180965600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr1:180940400-180988400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr1:180943000-180957400	Weak transcription	Fetal Heart	heart
8	chr1:180943600-180955600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr1:180943600-180972000	Weak transcription	Psoas Muscle	Psoas
10	chr1:180943600-180979800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr1:180944400-180962600	Strong transcription	Osteobl	bone
12	chr1:180944600-180957600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
13	chr1:180944800-180970800	Weak transcription	Pancreatic Islets	Pancreatic Islet
14	chr1:180945400-180975000	Strong transcription	Monocytes-CD14+_RO01746	blood
15	chr1:180945600-180974800	Strong transcription	Primary monocytes fromperipheralblood	blood
16	chr1:180945800-180956200	Weak transcription	Colonic Mucosa	Colon
17	chr1:180946000-180953800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr1:180946200-180954600	Weak transcription	NHLF	lung
19	chr1:180946600-180953400	Weak transcription	HUVEC	blood vessel
20	chr1:180946600-180954400	Weak transcription	Ovary	ovary
21	chr1:180946600-180955200	Weak transcription	Esophagus	oesophagus
22	chr1:180946800-180953400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr1:180946800-180955200	Weak transcription	Pancreas	Pancrea
24	chr1:180947200-180956000	Weak transcription	NH-A	brain
25	chr1:180947800-180954600	Weak transcription	Aorta	Aorta
26	chr1:180948200-180959400	Weak transcription	Stomach Mucosa	stomach
27	chr1:180948600-180961400	Strong transcription	Fetal Intestine Large	intestine
28	chr1:180948800-180959800	Strong transcription	Left Ventricle	heart
29	chr1:180948800-180961000	Strong transcription	Primary neutrophils fromperipheralblood	blood
30	chr1:180949000-180962400	Strong transcription	Fetal Muscle Trunk	muscle
31	chr1:180949000-180962600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr1:180949400-180957400	Strong transcription	Fetal Muscle Leg	muscle
33	chr1:180949400-180963800	Strong transcription	Liver	Liver
34	chr1:180949800-180962600	Strong transcription	Adipose Nuclei	Adipose
35	chr1:180949800-180962600	Strong transcription	Rectal Mucosa Donor 29	rectum
36	chr1:180949800-180963800	Strong transcription	Duodenum Mucosa	Duodenum
37	chr1:180949800-180966200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr1:180950000-180962600	Strong transcription	Skeletal Muscle Female	skeletal muscle
39	chr1:180950000-180964600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr1:180950000-180965200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr1:180950000-180966400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
42	chr1:180950000-180968200	Strong transcription	HMEC	breast
43	chr1:180950400-180954400	Weak transcription	Fetal Kidney	kidney
44	chr1:180950400-180956000	Weak transcription	Rectal Smooth Muscle	rectum
45	chr1:180950600-180962400	Strong transcription	Muscle Satellite Cultured Cells	--
46	chr1:180950800-180953400	Weak transcription	Spleen	Spleen
47	chr1:180950800-180953800	Weak transcription	H9 Cell Line	embryonic stem cell
48	chr1:180950800-180962400	Strong transcription	Placenta	Placenta
49	chr1:180951000-180957400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr1:180951200-180955600	Weak transcription	K562	blood

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