Variant report

Variant	rs7859478
Chromosome Location	chr9:117817405-117817406
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:117810151..117812770-chr9:117815287..117818009,2	K562	blood:

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10817710	0.80[CEU][hapmap]
rs10982497	0.81[CHB][hapmap];0.90[JPT][hapmap]
rs10982503	0.88[CHB][hapmap];0.91[JPT][hapmap];0.85[YRI][hapmap];0.88[ASN][1000 genomes]
rs10982504	0.88[ASN][1000 genomes]
rs10982509	0.89[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10982516	0.80[CEU][hapmap]
rs11788513	0.89[ASN][1000 genomes]
rs12235159	0.80[CEU][hapmap]
rs12338715	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12340324	0.80[CEU][hapmap]
rs12343737	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12344929	0.88[CEU][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs12346540	0.85[ASN][1000 genomes]
rs12347433	0.81[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.85[ASN][1000 genomes]
rs12348090	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12349585	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13285041	0.94[AFR][1000 genomes];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13286217	0.85[ASN][1000 genomes]
rs1411453	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1411455	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2274751	0.87[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs2274835	0.89[CEU][hapmap];0.93[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2297179	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2297181	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28491824	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34865477	0.94[AFR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3789871	0.89[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.94[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs3789875	0.87[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.88[ASN][1000 genomes]
rs4394462	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs66539628	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv831696	chr9:117701582-117874150	Weak transcription Enhancers Strong transcription Genic enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
2	nsv615250	chr9:117768021-118012841	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv916912	chr9:117770039-118014140	Flanking Active TSS Enhancers Strong transcription Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:117782400-117848200	Weak transcription	Brain Substantia Nigra	brain
2	chr9:117791600-117833200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr9:117799200-117819800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr9:117800800-117825000	Weak transcription	Fetal Muscle Leg	muscle
5	chr9:117800800-117825200	Weak transcription	Fetal Muscle Trunk	muscle
6	chr9:117801000-117819200	Weak transcription	HMEC	breast
7	chr9:117801800-117820200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr9:117802200-117848200	Weak transcription	Spleen	Spleen
9	chr9:117803400-117820000	Weak transcription	Aorta	Aorta
10	chr9:117803400-117820600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr9:117803600-117820200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr9:117803600-117825400	Weak transcription	Fetal Kidney	kidney
13	chr9:117805800-117818800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr9:117807400-117819600	Strong transcription	NHDF-Ad	bronchial
15	chr9:117807400-117819800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr9:117809000-117825400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr9:117809200-117821000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr9:117810000-117817600	Weak transcription	Fetal Stomach	stomach
19	chr9:117810200-117817600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr9:117810600-117825000	Weak transcription	Rectal Smooth Muscle	rectum
21	chr9:117812800-117819200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr9:117812800-117825800	Weak transcription	HUES64 Cell Line	embryonic stem cell
23	chr9:117812800-117830600	Weak transcription	Fetal Lung	lung
24	chr9:117813000-117817600	Weak transcription	NHEK	skin
25	chr9:117813200-117825000	Weak transcription	HUES6 Cell Line	embryonic stem cell
26	chr9:117813600-117819200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
27	chr9:117814400-117818000	Strong transcription	NHLF	lung
28	chr9:117815200-117817800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr9:117815200-117821000	Strong transcription	Cortex derived primary cultured neurospheres	brain
30	chr9:117815200-117825200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr9:117815400-117859200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
32	chr9:117816000-117817800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr9:117816000-117825200	Weak transcription	Esophagus	oesophagus
34	chr9:117816600-117818000	Genic enhancers	NH-A	brain
35	chr9:117816600-117819400	Strong transcription	Duodenum Smooth Muscle	Duodenum
36	chr9:117816600-117820600	Strong transcription	Colon Smooth Muscle	Colon
37	chr9:117816800-117817600	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr9:117816800-117817600	Genic enhancers	Osteobl	bone
39	chr9:117816800-117825000	Strong transcription	Stomach Smooth Muscle	stomach
40	chr9:117817000-117818800	Strong transcription	ES-I3 Cell Line	embryonic stem cell
41	chr9:117817000-117820400	Weak transcription	HSMM	muscle
42	chr9:117817200-117817600	Weak transcription	Placenta Amnion	Placenta Amnion
43	chr9:117817400-117819400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr9:117817400-117819800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr9:117817400-117820400	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links