Variant report

Variant	rs599312
Chromosome Location	chr9:27153536-27153537
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 21 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs480723	0.84[JPT][hapmap];0.87[ASN][1000 genomes]
rs507441	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs512118	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs512904	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs512964	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs514643	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs538679	0.95[CHB][hapmap];0.93[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs584451	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs584934	0.98[ASN][1000 genomes]
rs586284	1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs600728	0.84[JPT][hapmap];0.87[ASN][1000 genomes]
rs602112	0.84[JPT][hapmap];0.87[ASN][1000 genomes]
rs628873	0.82[ASN][1000 genomes]
rs664513	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7035021	0.83[GIH][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv892862	chr9:26956663-27190655	Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
2	nsv1016733	chr9:27073650-27264576	Enhancers Weak transcription Genic enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv1022313	chr9:27083369-27250505	Enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv1017802	chr9:27088160-27262682	Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv1019104	chr9:27088160-27358206	Enhancers Weak transcription Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
6	nsv892863	chr9:27138898-27170934	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs599312	IFT74	cis	parietal	SCAN
rs599312	PDDC1	trans	cerebellum	SCAN

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:27147800-27155000	Weak transcription	Aorta	Aorta
2	chr9:27149600-27154600	Enhancers	HUVEC	blood vessel
3	chr9:27149600-27155400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr9:27150800-27158000	Weak transcription	Spleen	Spleen
5	chr9:27151000-27154600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr9:27151000-27154800	Weak transcription	Placenta	Placenta
7	chr9:27151000-27155800	Enhancers	Placenta Amnion	Placenta Amnion
8	chr9:27151000-27158000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr9:27151000-27172800	Weak transcription	Left Ventricle	heart
10	chr9:27151000-27229200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr9:27151200-27164800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr9:27151400-27154600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr9:27151800-27154200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr9:27151800-27154600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
15	chr9:27151800-27158000	Weak transcription	Lung	lung
16	chr9:27151800-27165000	Weak transcription	Stomach Smooth Muscle	stomach
17	chr9:27152000-27155000	Weak transcription	Ovary	ovary
18	chr9:27152000-27174600	Weak transcription	Fetal Muscle Leg	muscle
19	chr9:27152200-27165400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr9:27152400-27153600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr9:27152400-27153600	Weak transcription	Skeletal Muscle Male	skeletal muscle
22	chr9:27152400-27154600	Weak transcription	Rectal Smooth Muscle	rectum
23	chr9:27152400-27154600	Weak transcription	NHLF	lung
24	chr9:27152400-27154800	Weak transcription	Fetal Stomach	stomach
25	chr9:27152400-27155000	Weak transcription	Fetal Lung	lung
26	chr9:27152400-27156600	Weak transcription	Hela-S3	cervix
27	chr9:27152400-27157800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
28	chr9:27152400-27181600	Weak transcription	Adipose Nuclei	Adipose
29	chr9:27152600-27153600	Weak transcription	HSMM	muscle
30	chr9:27152600-27154400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr9:27152600-27154400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr9:27152600-27154400	Weak transcription	Muscle Satellite Cultured Cells	--
33	chr9:27152600-27154400	Weak transcription	HMEC	breast
34	chr9:27152600-27154400	Weak transcription	NH-A	brain
35	chr9:27152600-27154400	Weak transcription	Osteobl	bone
36	chr9:27152600-27154600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr9:27152600-27154600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr9:27152600-27154600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr9:27152600-27154600	Weak transcription	Colon Smooth Muscle	Colon
40	chr9:27152600-27154600	Weak transcription	Fetal Heart	heart
41	chr9:27152800-27154200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr9:27153000-27154400	Weak transcription	NHEK	skin
43	chr9:27153200-27154400	Weak transcription	HSMMtube	muscle
44	chr9:27153200-27154600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links