Variant report

Variant	rs249006
Chromosome Location	chr5:79786405-79786406
allele	C/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	EP300	chr5:79786404-79786604	Hela-S3	cervix:	n/a	n/a
2	STAT3	chr5:79786313-79786606	Hela-S3	cervix:	n/a	n/a
3	BRCA1	chr5:79786393-79786586	Hela-S3	cervix:	n/a	n/a
4	TBP	chr5:79783533-79786711	Hela-S3	cervix:	n/a	n/a
5	CEBPB	chr5:79785360-79786561	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:79782822..79786705-chr5:79948261..79952248,11	MCF-7	breast:
2	chr5:79784731..79786261-chr5:79786333..79788295,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000249042	TF binding region
ENSG00000113318	Chromatin interaction
ENSG00000228716	Chromatin interaction

Extended variants
information (count: 122 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:120)

rs_ID	r²[population]
rs10433	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10474621	0.92[EUR][1000 genomes]
rs10474629	1.00[CEU][hapmap]
rs10942926	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1097307	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs1097308	0.85[ASN][1000 genomes]
rs1097309	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs1102116	1.00[ASN][1000 genomes]
rs1103116	0.87[ASN][1000 genomes]
rs1104243	0.81[EUR][1000 genomes]
rs13354660	1.00[JPT][hapmap];0.92[EUR][1000 genomes]
rs13359253	0.92[EUR][1000 genomes]
rs1363775	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs1423113	0.92[EUR][1000 genomes]
rs16877755	0.92[EUR][1000 genomes]
rs16877757	0.92[EUR][1000 genomes]
rs168938	0.85[ASN][1000 genomes]
rs168939	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs168940	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes]
rs171595	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs171596	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs171821	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs173597	1.00[ASN][1000 genomes]
rs173598	0.88[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs173599	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs174075	0.95[ASN][1000 genomes]
rs174076	1.00[CEU][hapmap];0.88[CHB][hapmap];0.88[YRI][hapmap];0.92[EUR][1000 genomes]
rs1820119	0.95[ASN][1000 genomes]
rs185100	0.88[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs187478	1.00[ASN][1000 genomes]
rs187479	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs192313	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs194540	0.83[ASN][1000 genomes]
rs194541	0.92[EUR][1000 genomes]
rs2251759	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs248995	0.85[CHB][hapmap]
rs248999	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs249000	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs249001	1.00[ASN][1000 genomes]
rs249003	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs249004	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs249005	1.00[ASN][1000 genomes]
rs249016	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs249020	0.83[ASN][1000 genomes]
rs249021	0.88[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs249023	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs249024	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs249025	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs249026	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs249027	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs249028	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs249029	1.00[ASN][1000 genomes]
rs249030	1.00[CHB][hapmap];0.83[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs249031	1.00[ASN][1000 genomes]
rs249032	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs249033	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs249037	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs249038	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs249039	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2544591	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs2544592	0.85[ASN][1000 genomes]
rs2544593	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs2544598	0.89[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2544599	0.95[ASN][1000 genomes]
rs2544600	0.86[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2544603	0.95[ASN][1000 genomes]
rs2544604	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2547487	0.85[ASN][1000 genomes]
rs259023	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.83[AFR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs259024	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.83[AFR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs259025	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs259026	0.83[AFR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs259027	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.83[AFR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs259028	1.00[CEU][hapmap];0.86[CHB][hapmap];0.87[YRI][hapmap];0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs259029	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs259030	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs259031	0.95[ASN][1000 genomes]
rs259032	0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs259033	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs259034	0.95[ASN][1000 genomes]
rs259036	0.92[EUR][1000 genomes]
rs259037	1.00[CEU][hapmap];0.86[CHB][hapmap];0.92[EUR][1000 genomes]
rs259038	1.00[CEU][hapmap];0.86[CHB][hapmap];0.92[EUR][1000 genomes]
rs259040	0.92[EUR][1000 genomes]
rs259042	1.00[CEU][hapmap];0.88[CHB][hapmap];0.92[EUR][1000 genomes]
rs259043	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs259044	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes]
rs259045	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes]
rs259046	0.92[EUR][1000 genomes]
rs259047	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes]
rs259048	1.00[CEU][hapmap];0.88[CHB][hapmap];0.88[EUR][1000 genomes]
rs259049	1.00[JPT][hapmap]
rs259051	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes]
rs259052	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs259053	1.00[CEU][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes]
rs259054	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes]
rs259055	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs2599508	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs28496723	0.92[EUR][1000 genomes]
rs28555465	0.92[EUR][1000 genomes]
rs3095851	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs3096111	0.80[ASN][1000 genomes]
rs394076	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs394170	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs399261	1.00[ASN][1000 genomes]
rs401612	0.95[ASN][1000 genomes]
rs408899	1.00[ASN][1000 genomes]
rs4704674	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs557346	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6869519	0.92[EUR][1000 genomes]
rs6885891	0.90[EUR][1000 genomes]
rs6887302	1.00[JPT][hapmap];0.90[EUR][1000 genomes]
rs6898411	1.00[CEU][hapmap]
rs701380	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs835726	0.82[AFR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs835729	0.83[AFR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs856765	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs856772	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs863163	1.00[ASN][1000 genomes]
rs969567	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:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:79784600-79787600	Weak transcription	Aorta	Aorta
2	chr5:79784600-79794600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr5:79784600-79797400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr5:79784800-79786600	Enhancers	iPS-18 Cell Line	embryonic stem cell
5	chr5:79784800-79788800	Weak transcription	HMEC	breast
6	chr5:79784800-79806600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr5:79784800-79819400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr5:79785000-79787600	Weak transcription	Primary neutrophils fromperipheralblood	blood
9	chr5:79785000-79788200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr5:79785000-79822800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr5:79785200-79788400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr5:79785200-79817600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr5:79785400-79788400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr5:79785400-79788400	Weak transcription	NHEK	skin
15	chr5:79785400-79788600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
16	chr5:79785400-79788800	Weak transcription	HUES48 Cell Line	embryonic stem cell
17	chr5:79785800-79786800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
18	chr5:79786200-79787000	Weak transcription	HSMMtube	muscle
19	chr5:79786200-79787200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr5:79786200-79787200	Weak transcription	Placenta	Placenta
21	chr5:79786200-79787400	Weak transcription	H1 Cell Line	embryonic stem cell
22	chr5:79786200-79788000	Enhancers	HepG2	liver
23	chr5:79786200-79790000	Weak transcription	Monocytes-CD14+_RO01746	blood
24	chr5:79786200-79790600	Weak transcription	Primary monocytes fromperipheralblood	blood
25	chr5:79786400-79786600	Flanking Active TSS	Hela-S3	cervix
26	chr5:79786400-79786800	Enhancers	HUES64 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links