Variant report

Variant	rs4132536
Chromosome Location	chr15:73358196-73358197
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	chr15:73356525..73360663-chr15:73369090..73372368,3	MCF-7	breast:

Extended variants
information (count: 74 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs1023924	1.00[CEU][hapmap];0.93[CHB][hapmap];0.91[CHD][hapmap];0.93[GIH][hapmap];0.94[JPT][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1038137	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs10467948	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs10467949	0.83[CHD][hapmap]
rs11072403	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11632639	0.83[JPT][hapmap]
rs12050774	0.93[CHB][hapmap];0.88[CHD][hapmap];0.91[GIH][hapmap];0.88[JPT][hapmap];0.83[MEX][hapmap];0.81[ASN][1000 genomes]
rs12899246	0.83[JPT][hapmap]
rs12902768	0.80[CHB][hapmap]
rs13379875	0.85[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.84[GIH][hapmap];0.88[JPT][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];0.89[MKK][hapmap];0.88[TSI][hapmap];0.95[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1479337	0.82[JPT][hapmap]
rs1479338	0.93[CHB][hapmap];0.88[JPT][hapmap]
rs1479339	0.93[CHB][hapmap];0.87[JPT][hapmap]
rs1479340	0.80[CHB][hapmap];0.83[CHD][hapmap];0.98[GIH][hapmap];0.81[JPT][hapmap];0.87[MEX][hapmap]
rs1564345	0.80[CHB][hapmap];0.83[CHD][hapmap];0.93[GIH][hapmap];0.87[MEX][hapmap]
rs17762146	0.85[CEU][hapmap];0.85[TSI][hapmap]
rs17762600	0.93[CHB][hapmap];0.91[CHD][hapmap];0.86[GIH][hapmap];0.88[JPT][hapmap];0.83[MEX][hapmap]
rs17829830	0.93[CHB][hapmap];0.91[CHD][hapmap];0.88[GIH][hapmap];0.88[JPT][hapmap]
rs17829957	0.93[CHB][hapmap];0.88[JPT][hapmap]
rs1871385	0.80[CHB][hapmap];0.91[CHD][hapmap]
rs2046017	0.83[CHD][hapmap]
rs2127277	0.80[CHB][hapmap];0.83[CHD][hapmap];0.93[GIH][hapmap];0.87[MEX][hapmap]
rs2169951	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2251205	0.83[CHD][hapmap]
rs2415147	0.80[CHB][hapmap];0.81[JPT][hapmap]
rs2415148	0.93[CHB][hapmap];0.88[JPT][hapmap]
rs2899784	0.88[CEU][hapmap];0.81[JPT][hapmap]
rs3736510	0.80[CHB][hapmap];0.91[CHD][hapmap];0.81[JPT][hapmap]
rs3784793	0.91[CHB][hapmap]
rs4132535	0.86[CHD][hapmap];0.83[JPT][hapmap]
rs4375637	0.86[CHB][hapmap]
rs4545783	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4609810	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4776624	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4776625	0.88[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs4777582	0.83[JPT][hapmap]
rs4777589	0.83[CHD][hapmap];0.83[JPT][hapmap]
rs4777590	0.96[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.93[TSI][hapmap];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4777591	0.83[JPT][hapmap]
rs55836604	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs55916847	0.90[EUR][1000 genomes]
rs55925663	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56269104	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56377702	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62016795	0.87[EUR][1000 genomes]
rs62016796	0.84[EUR][1000 genomes]
rs62016797	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62016803	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62016805	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62016806	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62016809	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62016811	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62016814	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62016849	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62016851	0.82[ASN][1000 genomes]
rs6495047	0.81[JPT][hapmap]
rs7164894	0.83[JPT][hapmap]
rs7165610	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7169083	0.80[CHB][hapmap];0.81[JPT][hapmap]
rs7172021	0.80[CHB][hapmap];0.83[CHD][hapmap];0.98[GIH][hapmap];0.87[MEX][hapmap]
rs7175329	0.83[CHD][hapmap];0.83[JPT][hapmap]
rs747872	0.80[CHB][hapmap]
rs747873	0.80[CHB][hapmap];0.91[CHD][hapmap]
rs8026121	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8026579	0.87[JPT][hapmap]
rs8042700	0.80[CHB][hapmap];0.81[JPT][hapmap]
rs922516	0.83[CHD][hapmap];0.83[JPT][hapmap]
rs9920186	0.86[CHD][hapmap];0.83[JPT][hapmap]
rs9972347	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3352103	chr15:73191535-73454001	Bivalent/Poised TSS Active TSS Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv482421	chr15:73279141-73426897	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
3	nsv904338	chr15:73313691-73483718	Enhancers Active TSS Strong transcription ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv517966	chr15:73349633-73488753	Enhancers Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv525462	chr15:73349633-73563495	Genic enhancers Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4132536	GRAMD2	cis	parietal	SCAN
rs4132536	CIITA	trans	parietal	SCAN
rs4132536	THAP10	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:73347000-73358800	Weak transcription	HUES64 Cell Line	embryonic stem cell
2	chr15:73349400-73367000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr15:73352000-73365000	Weak transcription	Skeletal Muscle Male	skeletal muscle
4	chr15:73353800-73363400	Weak transcription	Aorta	Aorta
5	chr15:73353800-73366000	Weak transcription	Fetal Intestine Large	intestine
6	chr15:73353800-73367400	Weak transcription	Fetal Intestine Small	intestine
7	chr15:73354000-73359000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
8	chr15:73354400-73364800	Weak transcription	Skeletal Muscle Female	skeletal muscle
9	chr15:73355200-73365200	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr15:73355600-73365800	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr15:73356400-73359000	Weak transcription	Brain Angular Gyrus	brain
12	chr15:73356600-73360200	Weak transcription	Brain Anterior Caudate	brain
13	chr15:73356800-73359000	Weak transcription	Brain Hippocampus Middle	brain
14	chr15:73357800-73359400	Enhancers	Brain Substantia Nigra	brain
15	chr15:73358000-73358800	Weak transcription	Brain Cingulate Gyrus	brain
16	chr15:73358000-73367000	Weak transcription	Brain Inferior Temporal Lobe	brain

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