Variant report

Variant	rs173597
Chromosome Location	chr5:79791605-79791606
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	chr5:79791201..79794183-chr5:79803550..79806446,2	MCF-7	breast:
2	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	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10942926	0.95[ASN][1000 genomes]
rs1097307	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1097308	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1097309	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1102116	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1103116	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1363775	0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs168938	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs168939	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs171595	1.00[ASN][1000 genomes]
rs171596	1.00[ASN][1000 genomes]
rs171821	0.80[EUR][1000 genomes]
rs173598	0.82[ASN][1000 genomes]
rs173599	0.95[ASN][1000 genomes]
rs174075	0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1820119	0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs185100	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs187478	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs187479	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs192313	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs194540	0.83[ASN][1000 genomes]
rs2251759	0.95[ASN][1000 genomes]
rs248995	0.96[EUR][1000 genomes]
rs248999	1.00[ASN][1000 genomes]
rs249000	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs249001	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs249003	1.00[ASN][1000 genomes]
rs249004	1.00[ASN][1000 genomes]
rs249005	0.84[AFR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs249006	1.00[ASN][1000 genomes]
rs249016	0.92[ASN][1000 genomes]
rs249020	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs249021	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs249023	0.95[ASN][1000 genomes]
rs249024	0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs249025	0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs249026	0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs249027	0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs249028	0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs249029	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs249030	1.00[ASN][1000 genomes]
rs249031	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs249032	1.00[ASN][1000 genomes]
rs249037	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs249038	0.95[ASN][1000 genomes]
rs249039	0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2544592	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2544593	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2544598	0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2544599	0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2544600	0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2544603	0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2544604	0.95[ASN][1000 genomes]
rs2547487	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs259023	0.85[ASN][1000 genomes]
rs259024	0.85[ASN][1000 genomes]
rs259025	0.85[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	0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs259032	0.95[ASN][1000 genomes]
rs259033	0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs259034	0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs259041	0.82[EUR][1000 genomes]
rs259043	0.80[EUR][1000 genomes]
rs259052	0.82[ASN][1000 genomes]
rs259055	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2599508	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3095851	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3096111	0.80[ASN][1000 genomes]
rs394076	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs394170	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs399261	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs401612	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs408899	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4704674	0.95[ASN][1000 genomes]
rs557346	1.00[ASN][1000 genomes]
rs701380	0.86[AMR][1000 genomes];0.92[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	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs969567	0.88[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:18 , 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	chr5:79787600-79795000	Enhancers	Primary neutrophils fromperipheralblood	blood
8	chr5:79789400-79793000	Weak transcription	HUES64 Cell Line	embryonic stem cell
9	chr5:79789400-79793200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr5:79790200-79793000	Weak transcription	HUES48 Cell Line	embryonic stem cell
11	chr5:79790200-79793400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr5:79790800-79794600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
13	chr5:79790800-79811200	Weak transcription	Placenta	Placenta
14	chr5:79791000-79794400	Weak transcription	H1 Cell Line	embryonic stem cell
15	chr5:79791200-79792000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr5:79791400-79791800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
17	chr5:79791400-79794400	Weak transcription	Monocytes-CD14+_RO01746	blood
18	chr5:79791400-79798000	Weak transcription	Primary monocytes fromperipheralblood	blood

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