Variant report

Variant	rs9989738
Chromosome Location	chr2:179129455-179129456
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:179122190..179123778-chr2:179127950..179129848,2	K562	blood:

Extended variants
information (count: 48 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs101266	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10197166	0.80[JPT][hapmap]
rs10203420	0.85[EUR][1000 genomes]
rs11680778	0.83[EUR][1000 genomes]
rs12469658	0.80[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs12473780	0.82[EUR][1000 genomes]
rs12474257	0.92[AFR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12476671	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12693160	0.81[EUR][1000 genomes]
rs13382421	0.82[EUR][1000 genomes]
rs13400415	1.00[YRI][hapmap]
rs1434080	0.80[EUR][1000 genomes]
rs147180	1.00[ASW][hapmap];0.96[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.88[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap]
rs2366157	0.80[JPT][hapmap]
rs333992	0.94[JPT][hapmap]
rs333993	0.94[JPT][hapmap]
rs333995	0.93[JPT][hapmap]
rs333996	0.81[JPT][hapmap]
rs333997	0.96[CEU][hapmap];0.95[CHB][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs333998	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs334000	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs334001	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs334002	1.00[JPT][hapmap]
rs334004	0.92[AFR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs334005	0.81[JPT][hapmap]
rs334007	0.81[JPT][hapmap]
rs334009	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs334013	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs334014	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.97[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs334017	0.81[JPT][hapmap]
rs334035	0.80[JPT][hapmap]
rs334040	0.81[JPT][hapmap]
rs334042	0.81[JPT][hapmap]
rs334045	0.81[JPT][hapmap]
rs334604	0.81[JPT][hapmap]
rs334616	0.88[JPT][hapmap]
rs551368	1.00[ASW][hapmap];0.96[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];0.88[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6719178	0.80[JPT][hapmap]
rs6756651	0.82[JPT][hapmap]
rs7419749	0.86[ASW][hapmap]
rs7587549	0.80[EUR][1000 genomes]
rs7599683	0.82[JPT][hapmap]
rs9288016	0.88[EUR][1000 genomes]
rs9288017	0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1009312	chr2:178924318-179215566	Weak transcription Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv536057	chr2:178924318-179215566	Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv875452	chr2:178963445-179167766	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv1011423	chr2:179084407-179166160	Enhancers Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9989738	LOC100130691	cis	cerebellum	SCAN
rs9989738	LOC100128288	trans	parietal	SCAN

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:179111200-179137400	Weak transcription	Right Atrium	heart
2	chr2:179124000-179130800	Weak transcription	Psoas Muscle	Psoas
3	chr2:179124200-179133200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr2:179124800-179134400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr2:179126000-179136600	Weak transcription	Aorta	Aorta
6	chr2:179127800-179130000	Enhancers	K562	blood
7	chr2:179129200-179130800	Weak transcription	Skeletal Muscle Female	skeletal muscle
8	chr2:179129400-179130800	Weak transcription	Skeletal Muscle Male	skeletal muscle

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