Variant report

Variant	rs9864775
Chromosome Location	chr3:135643568-135643569
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	chr3:135641417..135644037-chr3:135644616..135646188,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000242222	Chromatin interaction

Extended variants
information (count: 104 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:101)

rs_ID	r²[population]
rs10048942	1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs10049233	0.92[ASN][1000 genomes]
rs10512981	1.00[CEU][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10935175	1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs13082684	0.92[ASN][1000 genomes]
rs13097946	0.80[CEU][hapmap];1.00[JPT][hapmap]
rs13098245	1.00[JPT][hapmap]
rs13322891	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13325914	1.00[JPT][hapmap]
rs13434196	1.00[CEU][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1356664	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1401545	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1403766	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1403767	1.00[ASN][1000 genomes]
rs1403770	1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs1568349	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1568350	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16843509	1.00[CEU][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17197552	0.81[CEU][hapmap];1.00[JPT][hapmap]
rs2204259	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28449384	0.87[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs28570106	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28576629	0.92[ASN][1000 genomes]
rs28855968	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28875187	1.00[ASN][1000 genomes]
rs34522617	0.84[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs34767379	0.92[ASN][1000 genomes]
rs35722356	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36039354	0.92[ASN][1000 genomes]
rs4718	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55678980	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56308637	1.00[ASN][1000 genomes]
rs56807950	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs59063369	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs66544356	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6771997	0.81[CEU][hapmap];1.00[JPT][hapmap]
rs6773469	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6774289	0.81[CEU][hapmap];1.00[JPT][hapmap]
rs6775778	1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs6779603	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6802139	1.00[CEU][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6807058	1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs6807242	1.00[JPT][hapmap]
rs6807565	0.84[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs6809006	0.81[CEU][hapmap];1.00[JPT][hapmap]
rs73222222	0.92[ASN][1000 genomes]
rs7427833	0.84[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs7433567	0.81[CEU][hapmap];0.84[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs7609938	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7621331	0.81[CEU][hapmap];1.00[JPT][hapmap]
rs7621396	1.00[JPT][hapmap];0.87[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs7621425	1.00[JPT][hapmap]
rs7626676	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7628848	0.92[ASN][1000 genomes]
rs7638129	1.00[CEU][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7640153	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7641070	0.92[ASN][1000 genomes]
rs7643661	1.00[JPT][hapmap]
rs870812	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs908825	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9289503	1.00[JPT][hapmap]
rs9808979	0.81[CEU][hapmap];1.00[JPT][hapmap]
rs9812561	1.00[JPT][hapmap]
rs9813082	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9814505	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9814557	0.81[CEU][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs9819440	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9819988	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9820189	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9824558	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9825239	1.00[JPT][hapmap];0.87[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs9826806	0.81[CEU][hapmap];1.00[JPT][hapmap]
rs9829329	1.00[CEU][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9829476	1.00[CEU][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9833699	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9833799	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9834624	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9836374	1.00[JPT][hapmap]
rs9836758	1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs9837855	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9839259	1.00[CEU][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9842840	1.00[JPT][hapmap]
rs9842864	0.92[ASN][1000 genomes]
rs9843725	0.80[CEU][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs9844478	1.00[CEU][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9846137	0.81[CEU][hapmap]
rs9848322	1.00[JPT][hapmap];0.90[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs9849088	1.00[CEU][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9853577	1.00[JPT][hapmap];0.87[AFR][1000 genomes]
rs9854494	1.00[CEU][hapmap];1.00[JPT][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9862264	1.00[JPT][hapmap]
rs9862777	0.84[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs9864247	1.00[JPT][hapmap]
rs9864656	1.00[CEU][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9868246	0.81[CEU][hapmap]
rs9870581	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9872542	0.81[CEU][hapmap];1.00[JPT][hapmap]
rs9875948	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9876837	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9877722	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9883808	0.85[CEU][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv460860	chr3:135107678-135769006	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv591829	chr3:135107678-135769006	Flanking Active TSS Strong transcription Active TSS Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
3	nsv829732	chr3:135561706-135756840	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:135641200-135645800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr3:135641800-135645600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr3:135642000-135645600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr3:135642000-135645600	Weak transcription	NHDF-Ad	bronchial
5	chr3:135642000-135646000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr3:135642200-135643600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr3:135642200-135645400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr3:135642200-135645400	Weak transcription	NHEK	skin
9	chr3:135642200-135645600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr3:135642200-135646000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr3:135642400-135645400	Weak transcription	HMEC	breast
12	chr3:135643200-135643600	Enhancers	Placenta	Placenta
13	chr3:135643400-135643600	Enhancers	Pancreas	Pancrea
14	chr3:135643400-135644000	Enhancers	H9 Cell Line	embryonic stem cell

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