Variant report

Variant	rs202516
Chromosome Location	chr20:1704837-1704838
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 86 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:78)

rs_ID	r²[population]
rs12625431	0.80[CHB][hapmap]
rs1438106	0.81[CHB][hapmap]
rs1550265	0.89[CHB][hapmap]
rs1550266	0.81[CHB][hapmap]
rs169354	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs202464	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs202465	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs202472	0.92[ASN][1000 genomes]
rs202474	0.92[ASN][1000 genomes]
rs202475	0.92[ASN][1000 genomes]
rs202476	0.91[ASN][1000 genomes]
rs202477	0.90[ASN][1000 genomes]
rs202493	0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs202494	1.00[ASN][1000 genomes]
rs202495	1.00[ASN][1000 genomes]
rs202496	1.00[ASN][1000 genomes]
rs202497	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs202498	1.00[ASN][1000 genomes]
rs202499	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs202500	1.00[ASN][1000 genomes]
rs202501	1.00[ASN][1000 genomes]
rs202502	1.00[ASN][1000 genomes]
rs202503	1.00[ASN][1000 genomes]
rs202504	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs202505	1.00[ASN][1000 genomes]
rs202506	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs202511	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs202512	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs202513	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs202517	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs202519	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs202551	0.85[CHB][hapmap];0.83[CHD][hapmap];0.81[JPT][hapmap]
rs202552	0.80[CHB][hapmap]
rs2247997	0.97[ASN][1000 genomes]
rs4254564	0.81[CHB][hapmap]
rs4254566	0.80[CHB][hapmap]
rs4353709	0.81[CHB][hapmap]
rs4473456	0.81[CHB][hapmap]
rs480743	0.98[ASN][1000 genomes]
rs480769	0.98[ASN][1000 genomes]
rs482716	0.98[ASN][1000 genomes]
rs493466	0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs497134	0.91[ASN][1000 genomes]
rs498139	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs513119	0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs513201	0.98[ASN][1000 genomes]
rs514813	0.98[ASN][1000 genomes]
rs514965	0.81[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs515883	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs515973	0.81[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs517578	1.00[CHB][hapmap];0.88[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.87[TSI][hapmap];0.98[ASN][1000 genomes]
rs528256	0.98[ASN][1000 genomes]
rs532097	0.98[ASN][1000 genomes]
rs544110	0.81[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs549733	0.97[ASN][1000 genomes]
rs572620	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs577238	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs578127	0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs578970	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs585046	0.97[ASN][1000 genomes]
rs588555	0.88[ASN][1000 genomes]
rs599837	1.00[CHB][hapmap];0.88[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.87[TSI][hapmap];0.81[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs600303	1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.80[YRI][hapmap];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs601652	0.81[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs6034368	0.81[CHB][hapmap]
rs6034370	0.80[CHB][hapmap]
rs6043722	0.81[CHB][hapmap]
rs6043726	0.80[CHB][hapmap]
rs6044192	0.82[ASN][1000 genomes]
rs615007	0.98[ASN][1000 genomes]
rs629812	0.98[ASN][1000 genomes]
rs629867	0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs629878	0.98[ASN][1000 genomes]
rs648051	0.92[ASN][1000 genomes]
rs659348	0.92[ASN][1000 genomes]
rs679310	0.83[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs692847	0.92[ASN][1000 genomes]
rs692891	0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv585206	chr20:1386473-1714362	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	nsv912596	chr20:1486637-1877150	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
3	nsv1057036	chr20:1493425-1869281	Weak transcription Flanking Bivalent TSS/Enh Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
4	nsv912597	chr20:1500506-1877150	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
5	nsv833894	chr20:1519433-1753366	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
6	nsv531473	chr20:1532476-1864506	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
7	nsv1063429	chr20:1679052-1706969	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Strong transcription	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
8	nsv962538	chr20:1702183-1716952	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs202516	HSPA12B	cis	cerebellum	SCAN

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:1701400-1714600	Weak transcription	Brain Hippocampus Middle	brain
2	chr20:1702600-1707000	Weak transcription	Primary neutrophils fromperipheralblood	blood
3	chr20:1703400-1720200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr20:1704800-1705000	Enhancers	Monocytes-CD14+_RO01746	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links