Variant report

Variant	rs10989471
Chromosome Location	chr9:104069201-104069202
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:104068294..104070576-chr9:104071673..104073236,2	MCF-7	breast:

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10125731	0.92[CEU][hapmap];0.94[CHB][hapmap];0.84[JPT][hapmap];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10512279	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10989462	0.81[JPT][hapmap]
rs10989469	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11790209	1.00[CHB][hapmap];0.90[JPT][hapmap];0.97[ASN][1000 genomes]
rs11790501	0.84[ASN][1000 genomes]
rs11792655	0.88[CHB][hapmap];0.85[JPT][hapmap];0.83[ASN][1000 genomes]
rs12341244	0.81[JPT][hapmap]
rs12341316	0.80[JPT][hapmap]
rs12553209	0.88[ASN][1000 genomes]
rs12553507	0.87[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs12683393	0.80[CEU][hapmap];0.94[CHB][hapmap];0.90[JPT][hapmap];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12683674	0.92[CEU][hapmap];0.94[JPT][hapmap];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12684829	0.94[CHB][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs13289023	0.80[JPT][hapmap]
rs13296052	0.80[JPT][hapmap]
rs1341769	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1891219	1.00[CHB][hapmap];0.90[JPT][hapmap];0.97[ASN][1000 genomes]
rs1935240	0.94[CHB][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs2275683	0.96[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34553293	0.85[ASN][1000 genomes]
rs35846126	0.97[ASN][1000 genomes]
rs3780531	0.94[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs3944892	0.80[JPT][hapmap]
rs4480176	0.95[ASN][1000 genomes]
rs6479049	0.92[CEU][hapmap];0.88[CHB][hapmap];0.88[JPT][hapmap];0.87[ASN][1000 genomes]
rs7023799	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7034058	0.80[JPT][hapmap]
rs7040055	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7848242	0.94[CHB][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs7861116	0.89[ASN][1000 genomes]
rs7865487	0.94[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7868832	0.94[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs7869625	0.94[CHB][hapmap];0.95[JPT][hapmap];0.86[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	nsv1037157	chr9:104045761-104149233	Enhancers Active TSS Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv1049740	chr9:104049624-104075825	Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:104048800-104071600	Weak transcription	Brain Inferior Temporal Lobe	brain
2	chr9:104068200-104071800	Weak transcription	HepG2	liver
3	chr9:104068400-104069800	Enhancers	Fetal Muscle Leg	muscle
4	chr9:104068400-104070800	Enhancers	Breast Myoepithelial Primary Cells	Breast
5	chr9:104068600-104069400	Enhancers	Fetal Brain Male	brain
6	chr9:104069000-104069800	Enhancers	Adipose Nuclei	Adipose
7	chr9:104069000-104070800	Enhancers	HMEC	breast
8	chr9:104069200-104069400	Enhancers	Aorta	Aorta
9	chr9:104069200-104069600	Enhancers	Cortex derived primary cultured neurospheres	brain
10	chr9:104069200-104069800	Enhancers	Brain Anterior Caudate	brain
11	chr9:104069200-104069800	Enhancers	Brain Germinal Matrix	brain
12	chr9:104069200-104069800	Enhancers	Esophagus	oesophagus
13	chr9:104069200-104070000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
14	chr9:104069200-104070800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr9:104069200-104070800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr9:104069200-104070800	Enhancers	NHEK	skin

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