Variant report

Variant	rs1041985
Chromosome Location	chr18:25543387-25543388
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr18:25533605..25535120-chr18:25543088..25545294,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000227279	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs1220154	0.91[CEU][hapmap];0.93[GIH][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1220155	0.81[JPT][hapmap];0.83[ASN][1000 genomes]
rs1220156	0.96[CEU][hapmap];0.83[CHD][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];0.95[MEX][hapmap];0.84[MKK][hapmap];0.95[TSI][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1220157	0.96[CEU][hapmap];0.87[CHB][hapmap];0.95[JPT][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17522096	0.96[CEU][hapmap];0.87[CHB][hapmap];0.95[JPT][hapmap]
rs1785613	0.87[CHB][hapmap];0.87[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.92[MEX][hapmap];0.91[TSI][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1785615	1.00[CEU][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2034108	0.96[CEU][hapmap];0.87[CHB][hapmap];0.91[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.88[MEX][hapmap];0.93[TSI][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4363925	0.84[CHD][hapmap];0.91[LWK][hapmap];0.88[MEX][hapmap];0.90[TSI][hapmap];0.93[YRI][hapmap];0.83[AMR][1000 genomes]
rs4413048	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2761996	chr18:24866083-25818618	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
2	esv2760473	chr18:25386088-25571466	Enhancers Weak transcription Genic enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
3	nsv1066192	chr18:25454413-25606736	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
4	nsv543669	chr18:25454413-25606736	Enhancers Genic enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
5	nsv833605	chr18:25467096-25643447	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:25528600-25547600	Weak transcription	HepG2	liver
2	chr18:25530800-25555400	Weak transcription	Brain Cingulate Gyrus	brain
3	chr18:25531000-25544800	Weak transcription	HUVEC	blood vessel
4	chr18:25531000-25548000	Weak transcription	Right Ventricle	heart
5	chr18:25531200-25593600	Weak transcription	Fetal Kidney	kidney
6	chr18:25532600-25545000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr18:25534600-25546800	Weak transcription	Fetal Lung	lung
8	chr18:25535000-25543800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr18:25535000-25544400	Strong transcription	NH-A	brain
10	chr18:25535200-25543600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr18:25535800-25545800	Strong transcription	Liver	Liver
12	chr18:25536400-25578200	Weak transcription	Fetal Brain Male	brain
13	chr18:25536600-25545400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr18:25536600-25554200	Weak transcription	HSMMtube	muscle
15	chr18:25536800-25574200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr18:25537000-25544800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr18:25537400-25543800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr18:25537400-25545800	Strong transcription	Osteobl	bone
19	chr18:25537600-25543400	Strong transcription	Fetal Brain Female	brain
20	chr18:25537600-25543600	Strong transcription	HUES64 Cell Line	embryonic stem cell
21	chr18:25538200-25548200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr18:25538800-25547400	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr18:25540000-25544600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr18:25540000-25544800	Strong transcription	Muscle Satellite Cultured Cells	--
25	chr18:25540200-25564600	Weak transcription	Ovary	ovary
26	chr18:25540400-25545200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr18:25540400-25547600	Strong transcription	HSMM	muscle
28	chr18:25540600-25548200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr18:25540600-25554600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
30	chr18:25540600-25555200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr18:25540800-25544800	Weak transcription	Brain Anterior Caudate	brain
32	chr18:25540800-25555800	Weak transcription	Brain Angular Gyrus	brain
33	chr18:25540800-25564400	Weak transcription	Brain Hippocampus Middle	brain
34	chr18:25540800-25576400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr18:25541000-25544400	Weak transcription	HUES6 Cell Line	embryonic stem cell
36	chr18:25541200-25544200	Weak transcription	A549	lung
37	chr18:25541400-25543600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr18:25541400-25544600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
39	chr18:25541400-25548000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr18:25541600-25544800	Weak transcription	Left Ventricle	heart
41	chr18:25541600-25547600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr18:25541600-25552400	Weak transcription	Dnd41	blood
43	chr18:25541600-25555400	Weak transcription	Aorta	Aorta
44	chr18:25541800-25545600	Weak transcription	Brain Substantia Nigra	brain
45	chr18:25542600-25543400	Strong transcription	HUES48 Cell Line	embryonic stem cell
46	chr18:25542600-25543600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
47	chr18:25542800-25543800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr18:25542800-25544000	Strong transcription	Fetal Heart	heart
49	chr18:25542800-25574400	Strong transcription	Cortex derived primary cultured neurospheres	brain
50	chr18:25543000-25543400	Strong transcription	Brain Germinal Matrix	brain

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