Variant report

Variant	rs4278208
Chromosome Location	chr9:103929779-103929780
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 50 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10119316	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1019873	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10512278	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10989419	1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[ASN][1000 genomes]
rs12341807	1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12344899	0.93[ASN][1000 genomes]
rs12344900	0.93[ASN][1000 genomes]
rs12352148	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12555441	1.00[YRI][hapmap]
rs1367754	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.82[TSI][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1431472	1.00[CHB][hapmap];0.93[ASN][1000 genomes]
rs17761685	0.93[CEU][hapmap];0.94[CHD][hapmap];0.89[MKK][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17762396	1.00[CEU][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17829436	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17829926	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17831028	1.00[YRI][hapmap]
rs1987400	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3983746	1.00[CEU][hapmap];0.80[MEX][hapmap];0.82[TSI][hapmap]
rs41274975	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4342669	1.00[CHB][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4742806	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[YRI][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4743445	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4743446	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4743449	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4743450	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55672230	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs55903434	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56156225	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57097151	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57409431	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs58088765	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs58422308	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60195477	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60390009	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61489062	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61647398	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66858224	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs72741426	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs72741430	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72741431	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs72741437	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72741438	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72741439	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72741444	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72741445	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72741449	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs72741452	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7852006	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[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	nsv831671	chr9:103858107-104020816	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv948791	chr9:103893030-103964650	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4278208	C9orf125	cis	parietal	SCAN

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:103925200-103929800	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr9:103928400-103930600	Enhancers	Brain Hippocampus Middle	brain
3	chr9:103928600-103930600	Enhancers	Brain Cingulate Gyrus	brain
4	chr9:103929000-103929800	Enhancers	Fetal Kidney	kidney
5	chr9:103929000-103930000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr9:103929000-103930200	Enhancers	iPS-18 Cell Line	embryonic stem cell
7	chr9:103929000-103930200	Enhancers	Brain Inferior Temporal Lobe	brain
8	chr9:103929000-103930200	Enhancers	Brain Substantia Nigra	brain
9	chr9:103929000-103930200	Enhancers	Fetal Brain Female	brain
10	chr9:103929000-103930600	Enhancers	Cortex derived primary cultured neurospheres	brain
11	chr9:103929000-103930600	Enhancers	Brain Angular Gyrus	brain
12	chr9:103929000-103930800	Enhancers	Brain Anterior Caudate	brain
13	chr9:103929000-103931200	Enhancers	HepG2	liver
14	chr9:103929200-103930000	Enhancers	HUES64 Cell Line	embryonic stem cell
15	chr9:103929200-103930000	Enhancers	Breast Myoepithelial Primary Cells	Breast
16	chr9:103929200-103930000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
17	chr9:103929200-103930000	Enhancers	Fetal Brain Male	brain
18	chr9:103929200-103930200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr9:103929200-103930800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
20	chr9:103929400-103929800	Enhancers	H1 Cell Line	embryonic stem cell
21	chr9:103929400-103930000	Enhancers	HUES48 Cell Line	embryonic stem cell
22	chr9:103929600-103930000	Enhancers	Liver	Liver

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