Variant report

Variant	rs249001
Chromosome Location	chr5:79789545-79789546
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	chr5:79783897..79786252-chr5:79789316..79792239,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000152380	Chromatin interaction

Extended variants
information (count: 90 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:88)

rs_ID	r²[population]
rs10433	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10942926	0.95[ASN][1000 genomes]
rs1097307	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1097308	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1097309	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1102116	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1103116	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1363775	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs168938	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs168939	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs171595	1.00[ASN][1000 genomes]
rs171596	1.00[ASN][1000 genomes]
rs171821	0.83[EUR][1000 genomes]
rs173597	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs173598	0.82[ASN][1000 genomes]
rs173599	0.95[ASN][1000 genomes]
rs174075	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1820119	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs185100	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs187478	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs187479	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs192313	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs194540	0.83[ASN][1000 genomes]
rs2251759	0.95[ASN][1000 genomes]
rs248995	0.93[EUR][1000 genomes]
rs248999	1.00[ASN][1000 genomes]
rs249000	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs249003	1.00[ASN][1000 genomes]
rs249004	1.00[ASN][1000 genomes]
rs249005	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs249006	1.00[ASN][1000 genomes]
rs249016	0.92[ASN][1000 genomes]
rs249020	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs249021	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs249023	0.95[ASN][1000 genomes]
rs249024	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs249025	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs249026	0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs249027	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs249028	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs249029	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs249030	1.00[ASN][1000 genomes]
rs249031	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs249032	1.00[ASN][1000 genomes]
rs249037	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs249038	0.95[ASN][1000 genomes]
rs249039	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2544592	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2544593	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2544598	0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2544599	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2544600	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2544603	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2544604	0.95[ASN][1000 genomes]
rs2547487	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs259023	0.85[ASN][1000 genomes]
rs259024	0.85[ASN][1000 genomes]
rs259025	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs259026	0.85[ASN][1000 genomes]
rs259027	0.85[ASN][1000 genomes]
rs259028	0.95[ASN][1000 genomes]
rs259029	0.95[ASN][1000 genomes]
rs259030	0.95[ASN][1000 genomes]
rs259031	0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs259032	0.95[ASN][1000 genomes]
rs259033	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs259034	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs259041	0.84[EUR][1000 genomes]
rs259043	0.83[EUR][1000 genomes]
rs259052	0.82[ASN][1000 genomes]
rs259055	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2599508	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3095851	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3096111	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs394076	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs394170	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs399261	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs401612	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs408899	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4704674	0.95[ASN][1000 genomes]
rs557346	1.00[ASN][1000 genomes]
rs701380	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs835726	0.82[ASN][1000 genomes]
rs835729	0.87[ASN][1000 genomes]
rs856765	0.95[ASN][1000 genomes]
rs856772	1.00[ASN][1000 genomes]
rs863163	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs969567	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948807	chr5:79549207-79805765	Genic enhancers Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
2	nsv1028027	chr5:79694699-79841752	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:79784600-79794600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr5:79784600-79797400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr5:79784800-79806600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr5:79784800-79819400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr5:79785000-79822800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr5:79785200-79817600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr5:79786200-79790000	Weak transcription	Monocytes-CD14+_RO01746	blood
8	chr5:79786200-79790600	Weak transcription	Primary monocytes fromperipheralblood	blood
9	chr5:79787400-79791000	Enhancers	H1 Cell Line	embryonic stem cell
10	chr5:79787600-79795000	Enhancers	Primary neutrophils fromperipheralblood	blood
11	chr5:79787800-79791400	Enhancers	iPS-18 Cell Line	embryonic stem cell
12	chr5:79788200-79789600	Enhancers	Placenta	Placenta
13	chr5:79788400-79790200	Enhancers	NHEK	skin
14	chr5:79788800-79790200	Enhancers	HMEC	breast
15	chr5:79789200-79789600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr5:79789200-79790000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr5:79789200-79790000	Weak transcription	HSMMtube	muscle
18	chr5:79789200-79790400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr5:79789400-79789800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
20	chr5:79789400-79789800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr5:79789400-79790200	Enhancers	HUES48 Cell Line	embryonic stem cell
22	chr5:79789400-79790200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr5:79789400-79793000	Weak transcription	HUES64 Cell Line	embryonic stem cell
24	chr5:79789400-79793200	Weak transcription	iPS-15b Cell Line	embryonic stem cell

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