Variant report

Variant	rs7709149
Chromosome Location	chr5:80599578-80599579
allele	A/G
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	FOXA2	chr5:80599446-80599665	HepG2	liver:	n/a	n/a
2	ARID3A	chr5:80599488-80599712	HepG2	liver:	n/a	n/a
3	MYC	chr5:80599397-80599645	MCF10A-Er-Src	breast:	n/a	n/a
4	STAT3	chr5:80599345-80599682	MCF10A-Er-Src	breast:	n/a	n/a
5	POLR2A	chr5:80599352-80599683	MCF10A-Er-Src	breast:	n/a	n/a
6	POLR2A	chr5:80599096-80599802	PANC-1	pancreas:	n/a	n/a
7	FOS	chr5:80599352-80599742	MCF10A-Er-Src	breast:	n/a	n/a
8	FOS	chr5:80599346-80599797	MCF10A-Er-Src	breast:	n/a	n/a
9	FOS	chr5:80599397-80599712	MCF10A-Er-Src	breast:	n/a	n/a
10	POLR2A	chr5:80599305-80600190	MCF10A-Er-Src	breast:	n/a	n/a
11	RCOR1	chr5:80599177-80600177	IMR90	lung:	n/a	n/a
12	STAT3	chr5:80599450-80599677	MCF10A-Er-Src	breast:	n/a	n/a
13	FOXA1	chr5:80599323-80599726	HepG2	liver:	n/a	chr5:80599631-80599646

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:80599288..80602129-chr5:80607036..80608849,2	K562	blood:
2	chr5:80598755..80600911-chr5:80604785..80606382,2	K562	blood:

Variant related genes	Relation type
CKMT2-AS1	TF binding region
ZCCHC9	TF binding region

Extended variants
information (count: 51 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10038684	0.83[ASN][1000 genomes]
rs10041063	1.00[CHB][hapmap];0.83[ASN][1000 genomes]
rs10052929	0.82[CEU][hapmap]
rs10053706	0.83[ASN][1000 genomes]
rs10056565	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10063615	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10066296	0.83[ASN][1000 genomes]
rs10078279	1.00[CHB][hapmap];0.83[ASN][1000 genomes]
rs10474656	0.83[ASN][1000 genomes]
rs10514213	1.00[CHB][hapmap]
rs1055383	1.00[CHB][hapmap];0.92[ASN][1000 genomes]
rs10942945	1.00[CHB][hapmap]
rs11950033	1.00[CHB][hapmap]
rs13362314	0.83[ASN][1000 genomes]
rs1566432	1.00[CHB][hapmap];0.83[ASN][1000 genomes]
rs1566433	0.82[CEU][hapmap]
rs17294418	1.00[CHB][hapmap]
rs2173697	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2270823	1.00[CHB][hapmap];0.83[ASN][1000 genomes]
rs2406556	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28464111	0.83[ASN][1000 genomes]
rs28650401	0.83[ASN][1000 genomes]
rs2897389	1.00[CHB][hapmap]
rs2897390	1.00[CHB][hapmap]
rs3756636	0.88[CEU][hapmap];0.82[TSI][hapmap]
rs4703827	1.00[CHB][hapmap]
rs4704707	1.00[CHB][hapmap]
rs4704710	1.00[CHB][hapmap];0.83[ASN][1000 genomes]
rs4704711	0.83[CEU][hapmap]
rs4704712	0.83[ASN][1000 genomes]
rs4704714	0.82[CEU][hapmap]
rs4704715	0.83[ASN][1000 genomes]
rs4704720	0.92[ASN][1000 genomes]
rs59132806	0.83[ASN][1000 genomes]
rs60488995	0.83[ASN][1000 genomes]
rs60904680	0.83[ASN][1000 genomes]
rs61244991	0.83[ASN][1000 genomes]
rs62365865	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs68077638	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6863732	0.82[CEU][hapmap]
rs6866499	1.00[CHB][hapmap]
rs6867884	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6885028	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6893467	1.00[CHB][hapmap];0.83[ASN][1000 genomes]
rs7709071	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7720009	1.00[CHB][hapmap];0.83[ASN][1000 genomes]
rs7734902	0.96[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];0.94[GIH][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs921928	1.00[CHB][hapmap]
rs9293841	1.00[CHB][hapmap];0.83[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	nsv1024844	chr5:79862428-80860430	Weak transcription Strong transcription Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv598750	chr5:80503528-80599578	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:80593800-80599800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr5:80598000-80599800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
3	chr5:80598000-80605200	Weak transcription	Ovary	ovary
4	chr5:80598200-80599600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr5:80598200-80612400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr5:80598400-80599600	Enhancers	Primary T helper naive cells from peripheral blood	blood
7	chr5:80598400-80599600	Enhancers	Cortex derived primary cultured neurospheres	brain
8	chr5:80598400-80599800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr5:80598400-80600600	Weak transcription	Colonic Mucosa	Colon
10	chr5:80598400-80600600	Weak transcription	Fetal Muscle Trunk	muscle
11	chr5:80598400-80600600	Weak transcription	Thymus	Thymus
12	chr5:80598400-80601200	Weak transcription	Esophagus	oesophagus
13	chr5:80598400-80604800	Weak transcription	Primary hematopoietic stem cells	blood
14	chr5:80598400-80605200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
15	chr5:80598400-80606800	Weak transcription	H1 Cell Line	embryonic stem cell
16	chr5:80598400-80606800	Weak transcription	Right Ventricle	heart
17	chr5:80598400-80611200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr5:80598600-80599600	Enhancers	Breast Myoepithelial Primary Cells	Breast
19	chr5:80598600-80599600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
20	chr5:80598600-80599800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr5:80598600-80599800	Enhancers	Primary T cells from cord blood	blood
22	chr5:80598600-80599800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
23	chr5:80598600-80599800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
24	chr5:80598600-80599800	Enhancers	Primary T killer memory cells from peripheral blood	blood
25	chr5:80598600-80599800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr5:80598600-80599800	Enhancers	Skeletal Muscle Male	skeletal muscle
27	chr5:80598600-80600000	Enhancers	NH-A	brain
28	chr5:80598600-80600200	Enhancers	Muscle Satellite Cultured Cells	--
29	chr5:80598600-80600200	Enhancers	Liver	Liver
30	chr5:80598600-80600200	Enhancers	HMEC	breast
31	chr5:80598600-80600200	Enhancers	Osteobl	bone
32	chr5:80598600-80600400	Weak transcription	HUES48 Cell Line	embryonic stem cell
33	chr5:80598600-80600600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr5:80598600-80600600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
35	chr5:80598600-80600600	Weak transcription	Primary monocytes fromperipheralblood	blood
36	chr5:80598600-80600600	Weak transcription	Primary neutrophils fromperipheralblood	blood
37	chr5:80598600-80600600	Weak transcription	Fetal Muscle Leg	muscle
38	chr5:80598600-80600600	Weak transcription	Fetal Thymus	thymus
39	chr5:80598600-80600600	Weak transcription	Rectal Mucosa Donor 29	rectum
40	chr5:80598600-80600600	Weak transcription	Sigmoid Colon	Sigmoid Colon
41	chr5:80598600-80600600	Weak transcription	Monocytes-CD14+_RO01746	blood
42	chr5:80598600-80600800	Weak transcription	H9 Cell Line	embryonic stem cell
43	chr5:80598600-80600800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
44	chr5:80598600-80600800	Weak transcription	Colon Smooth Muscle	Colon
45	chr5:80598600-80600800	Weak transcription	Fetal Intestine Large	intestine
46	chr5:80598600-80601200	Weak transcription	Spleen	Spleen
47	chr5:80598600-80604400	Weak transcription	Duodenum Smooth Muscle	Duodenum
48	chr5:80598600-80604400	Weak transcription	Psoas Muscle	Psoas
49	chr5:80598600-80604800	Weak transcription	Primary B cells from cord blood	blood
50	chr5:80598600-80605000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links