Variant report

Variant	rs9301975
Chromosome Location	chr13:95205884-95205885
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:95201752..95203295-chr13:95205384..95208174,2	MCF-7	breast:

Extended variants
information (count: 118 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:115)

rs_ID	r²[population]
rs1408995	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17181801	0.91[ASN][1000 genomes]
rs17181808	0.91[ASN][1000 genomes]
rs1886787	0.87[ASN][1000 genomes]
rs1886789	0.91[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.91[JPT][hapmap];0.83[MEX][hapmap];0.87[ASN][1000 genomes]
rs1891099	0.96[ASN][1000 genomes]
rs1891100	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.84[TSI][hapmap];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2389132	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2389133	0.87[ASN][1000 genomes]
rs2389134	0.91[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.88[ASN][1000 genomes]
rs2389135	0.92[ASN][1000 genomes]
rs2389137	0.89[ASN][1000 genomes]
rs2389138	0.89[ASN][1000 genomes]
rs2389139	0.96[ASN][1000 genomes]
rs2892688	0.92[ASN][1000 genomes]
rs34536649	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35570210	0.85[ASN][1000 genomes]
rs4142020	0.92[ASN][1000 genomes]
rs4142021	0.92[ASN][1000 genomes]
rs4411370	0.96[ASN][1000 genomes]
rs4442657	0.93[ASN][1000 genomes]
rs4553470	0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6492711	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6492714	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs717769	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7317805	0.91[ASN][1000 genomes]
rs7318895	0.90[ASN][1000 genomes]
rs7323407	0.90[ASN][1000 genomes]
rs7325171	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7326382	0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7327906	0.91[ASN][1000 genomes]
rs7329277	0.88[ASN][1000 genomes]
rs7330052	0.88[ASN][1000 genomes]
rs7330757	0.89[ASN][1000 genomes]
rs7334113	0.88[ASN][1000 genomes]
rs7334290	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7334716	0.88[ASN][1000 genomes]
rs7334829	0.88[ASN][1000 genomes]
rs7335126	0.88[ASN][1000 genomes]
rs7336995	0.90[ASN][1000 genomes]
rs7336997	0.90[ASN][1000 genomes]
rs7337026	0.88[ASN][1000 genomes]
rs7337275	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7338715	0.91[ASN][1000 genomes]
rs7338730	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7490774	0.88[ASN][1000 genomes]
rs7492025	0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs767925	0.92[ASN][1000 genomes]
rs7997227	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7998655	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8002991	0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9284279	0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9301971	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9301972	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9301973	0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9301974	0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9556376	0.87[ASN][1000 genomes]
rs9556377	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9556378	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9556379	0.87[ASN][1000 genomes]
rs9556380	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9556381	0.87[ASN][1000 genomes]
rs9556382	0.87[ASN][1000 genomes]
rs9556383	0.87[ASN][1000 genomes]
rs9556384	0.87[ASN][1000 genomes]
rs9556386	0.88[ASN][1000 genomes]
rs9556387	0.88[ASN][1000 genomes]
rs9556388	0.88[ASN][1000 genomes]
rs9556390	0.91[ASN][1000 genomes]
rs9556391	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9556392	0.91[ASN][1000 genomes]
rs9556397	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9556398	0.96[ASN][1000 genomes]
rs9561568	0.87[ASN][1000 genomes]
rs9561569	0.87[ASN][1000 genomes]
rs9561570	0.87[ASN][1000 genomes]
rs9561571	0.87[ASN][1000 genomes]
rs9561572	0.87[ASN][1000 genomes]
rs9561573	0.87[ASN][1000 genomes]
rs9561574	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9561575	0.87[ASN][1000 genomes]
rs9561576	0.87[ASN][1000 genomes]
rs9561577	0.91[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.91[JPT][hapmap];0.87[ASN][1000 genomes]
rs9561578	0.88[ASN][1000 genomes]
rs9561579	0.87[ASN][1000 genomes]
rs9561580	0.88[ASN][1000 genomes]
rs9561581	0.88[ASN][1000 genomes]
rs9561582	0.88[ASN][1000 genomes]
rs9561583	0.88[ASN][1000 genomes]
rs9561584	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9561588	0.88[ASN][1000 genomes]
rs9561589	0.90[ASN][1000 genomes]
rs9561591	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9561592	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9561593	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9561595	0.91[ASN][1000 genomes]
rs9561596	0.91[ASN][1000 genomes]
rs9561597	0.91[ASN][1000 genomes]
rs9561599	0.92[ASN][1000 genomes]
rs9561600	0.92[ASN][1000 genomes]
rs9561601	0.92[ASN][1000 genomes]
rs9561602	0.92[ASN][1000 genomes]
rs9561603	0.89[ASN][1000 genomes]
rs9561604	0.90[ASN][1000 genomes]
rs9561605	0.90[ASN][1000 genomes]
rs9561606	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9561619	0.94[ASN][1000 genomes]
rs9561620	0.96[ASN][1000 genomes]
rs9561621	0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9561622	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9561623	0.96[ASN][1000 genomes]
rs9561625	0.96[ASN][1000 genomes]
rs9561626	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9590029	0.92[ASN][1000 genomes]
rs9590030	0.92[ASN][1000 genomes]

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	esv34004	chr13:94906537-95392644	Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv562756	chr13:95178317-95238154	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
3	nsv832685	chr13:95179676-95279966	Active TSS Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs9301975	DZIP1	cis	cerebellum	SCAN
rs9301975	DCT	cis	cerebellum	SCAN
rs9301975	DCT	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:95202400-95208800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
2	chr13:95202600-95221400	Weak transcription	Gastric	stomach
3	chr13:95202800-95208000	Weak transcription	Adipose Nuclei	Adipose
4	chr13:95202800-95208200	Weak transcription	Brain Germinal Matrix	brain
5	chr13:95202800-95210400	Weak transcription	Thymus	Thymus
6	chr13:95202800-95221400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
7	chr13:95202800-95222000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr13:95202800-95223600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr13:95203000-95221200	Weak transcription	Duodenum Mucosa	Duodenum
10	chr13:95203000-95221400	Weak transcription	Fetal Intestine Small	intestine
11	chr13:95203000-95222400	Weak transcription	HUES6 Cell Line	embryonic stem cell
12	chr13:95203200-95220800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr13:95203200-95220800	Weak transcription	Fetal Intestine Large	intestine
14	chr13:95203200-95222200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
15	chr13:95203400-95222400	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr13:95203400-95222600	Weak transcription	A549	lung
17	chr13:95204800-95214000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr13:95205000-95206600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr13:95205000-95208600	Weak transcription	Placenta	Placenta
20	chr13:95205200-95211200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr13:95205600-95206600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr13:95205800-95206400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links