Variant report

Variant	rs9299414
Chromosome Location	chr9:96805568-96805569
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	chr9:96804294..96806133-chr9:96926083..96928857,2	K562	blood:
2	chr9:96792256..96795925-chr9:96803341..96805691,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000269946	Chromatin interaction
ENSG00000158079	Chromatin interaction

Extended variants
information (count: 74 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs10117457	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10122334	0.82[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10123954	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10429556	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10429603	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10435922	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10435924	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10739967	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10739969	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs10761308	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10761309	0.92[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10761313	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10761315	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs10821284	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10821285	0.96[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10821290	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10993037	0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10993041	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10993058	0.83[CEU][hapmap]
rs12351292	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12684427	0.89[CEU][hapmap];0.94[CHB][hapmap];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1316814	0.88[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1320547	0.89[CEU][hapmap];0.94[CHB][hapmap];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13299545	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1331216	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1331217	0.89[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1331218	0.88[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1331219	0.92[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1343995	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1360429	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1411860	0.89[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1418251	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1576640	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1590969	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1592153	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1832857	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1854835	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1933668	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1933669	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1933679	0.88[EUR][1000 genomes]
rs2026917	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2094927	0.92[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2150625	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2153058	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2153070	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2153792	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2211362	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2225458	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2226117	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35883789	0.85[EUR][1000 genomes]
rs3847307	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3996241	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4282631	0.92[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4406469	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4744307	0.82[EUR][1000 genomes]
rs4744308	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4744310	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4744314	0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4744316	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6479522	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6479527	0.84[CEU][hapmap]
rs6479528	0.84[CEU][hapmap]
rs6479529	0.93[ASN][1000 genomes]
rs7033481	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7033898	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7045643	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7858069	0.96[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7867253	0.86[EUR][1000 genomes]
rs7867925	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs914295	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs914296	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs914297	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs987511	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv893589	chr9:96624645-96884544	Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Weak transcription Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:96794200-96828000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr9:96794800-96805600	Weak transcription	HSMM	muscle
3	chr9:96795400-96823800	Weak transcription	Left Ventricle	heart
4	chr9:96798200-96822400	Weak transcription	Fetal Lung	lung
5	chr9:96800000-96818600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr9:96804400-96805600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr9:96804600-96805600	Enhancers	Skeletal Muscle Male	skeletal muscle
8	chr9:96804800-96805600	Enhancers	Brain Inferior Temporal Lobe	brain
9	chr9:96804800-96805600	Enhancers	Brain Substantia Nigra	brain
10	chr9:96805000-96805600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
11	chr9:96805200-96805600	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell

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