Variant report

Variant	rs6560515
Chromosome Location	chr9:79015404-79015405
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:79008991..79011604-chr9:79014498..79020251,6	K562	blood:
2	chr9:79007886..79011336-chr9:79013243..79018063,7	MCF-7	breast:
3	chr9:79014853..79017600-chr9:79074234..79077178,2	MCF-7	breast:
4	chr9:79009095..79011288-chr9:79015114..79018669,3	K562	blood:

Variant related genes	Relation type
ENSG00000135002	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10116800	0.96[CEU][hapmap];0.86[MEX][hapmap];0.93[TSI][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10118954	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10125012	0.89[AMR][1000 genomes]
rs10125667	0.89[AMR][1000 genomes]
rs10781360	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10869770	0.91[YRI][hapmap];0.88[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs10869771	0.86[ASW][hapmap];0.86[MEX][hapmap];0.87[MKK][hapmap];0.84[TSI][hapmap];0.84[YRI][hapmap]
rs10869774	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11144875	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11144878	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11144881	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11144887	0.96[CEU][hapmap];0.91[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11144894	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1129399	0.86[AMR][1000 genomes]
rs11548954	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11791951	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11793613	0.87[ASW][hapmap];0.95[LWK][hapmap];0.93[MEX][hapmap];0.81[MKK][hapmap];0.84[TSI][hapmap];0.92[YRI][hapmap];0.92[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs11794019	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12156473	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12375735	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12377856	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12377878	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12380522	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1324213	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1951910	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2377640	1.00[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2377641	0.82[CEU][hapmap];1.00[CHB][hapmap];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2501925	0.88[YRI][hapmap]
rs3187236	0.86[AMR][1000 genomes]
rs4571791	0.93[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs57480680	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs58136435	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs59424752	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61334567	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62567919	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62568690	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6560513	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6560516	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7023191	0.96[CEU][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7025942	0.86[AMR][1000 genomes]
rs7026067	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7029439	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7035385	0.82[ASW][hapmap];0.86[MEX][hapmap];0.84[TSI][hapmap];0.91[AMR][1000 genomes]
rs7037345	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7038009	0.80[ASW][hapmap];0.88[CEU][hapmap];0.86[MEX][hapmap];0.86[AMR][1000 genomes]
rs7040138	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7041690	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7047489	0.89[AMR][1000 genomes]
rs7049245	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7851616	0.86[AMR][1000 genomes]
rs7852884	0.86[AMR][1000 genomes]
rs7853410	0.86[AMR][1000 genomes]
rs7859327	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs7875575	0.86[AFR][1000 genomes];0.92[AMR][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	nsv869152	chr9:78742197-79583399	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv931033	chr9:78850330-79366454	Genic enhancers Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv893478	chr9:78933874-79101006	Weak transcription Genic enhancers Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
4	nsv893479	chr9:78971253-79275226	Weak transcription Strong transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
5	nsv972402	chr9:79012721-79015493	Weak transcription Enhancers	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:79010200-79017000	Weak transcription	NH-A	brain
2	chr9:79010600-79016600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr9:79010600-79016600	Weak transcription	NHLF	lung
4	chr9:79010600-79017000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr9:79010600-79017000	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr9:79010600-79018000	Weak transcription	HUVEC	blood vessel
7	chr9:79010600-79018400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr9:79010600-79019400	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr9:79010800-79018400	Weak transcription	Primary T helper cells fromperipheralblood	blood
10	chr9:79010800-79018400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
11	chr9:79010800-79018400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr9:79010800-79018400	Weak transcription	NHDF-Ad	bronchial
13	chr9:79011000-79018400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr9:79011000-79018400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr9:79011000-79018400	Weak transcription	Rectal Mucosa Donor 29	rectum
16	chr9:79011200-79018000	Weak transcription	Monocytes-CD14+_RO01746	blood
17	chr9:79011200-79018400	Weak transcription	Primary monocytes fromperipheralblood	blood
18	chr9:79011400-79016800	Weak transcription	Fetal Intestine Small	intestine
19	chr9:79014800-79015600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr9:79014800-79016000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr9:79015000-79016000	Enhancers	Hela-S3	cervix
22	chr9:79015200-79015600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr9:79015200-79015600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr9:79015200-79015800	Enhancers	Primary hematopoietic stem cells short term culture	blood
25	chr9:79015200-79016000	Enhancers	NHEK	skin
26	chr9:79015200-79016400	Enhancers	Placenta	Placenta
27	chr9:79015200-79016800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr9:79015200-79017200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr9:79015200-79019000	Enhancers	HepG2	liver
30	chr9:79015200-79019600	Enhancers	Rectal Mucosa Donor 31	rectum
31	chr9:79015400-79015600	Enhancers	HUES64 Cell Line	embryonic stem cell
32	chr9:79015400-79016000	Enhancers	ES-I3 Cell Line	embryonic stem cell
33	chr9:79015400-79016000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr9:79015400-79016000	Enhancers	HMEC	breast
35	chr9:79015400-79016800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr9:79015400-79016800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr9:79015400-79017400	Weak transcription	GM12878-XiMat	blood
38	chr9:79015400-79018200	Enhancers	A549	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links