Variant report

Variant	rs1905864
Chromosome Location	chr3:59781217-59781218
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 27 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs11130734	0.84[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.95[JPT][hapmap];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1352022	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1905865	0.95[CHB][hapmap];0.90[JPT][hapmap];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2046454	0.94[ASN][1000 genomes]
rs2629878	0.94[ASN][1000 genomes]
rs2629879	0.95[ASN][1000 genomes]
rs2629881	0.94[ASN][1000 genomes]
rs34764324	0.93[ASN][1000 genomes]
rs4455289	0.86[ASN][1000 genomes]
rs562516	0.95[CHB][hapmap];1.00[CHD][hapmap];0.85[JPT][hapmap];0.96[ASN][1000 genomes]
rs565226	0.85[JPT][hapmap]
rs606415	0.97[ASN][1000 genomes]
rs66805688	0.94[ASN][1000 genomes]
rs670592	1.00[JPT][hapmap]
rs67367323	0.94[ASN][1000 genomes]
rs6774343	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs67777617	0.90[ASN][1000 genomes]
rs6781354	1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs683809	0.97[ASN][1000 genomes]
rs9311726	1.00[CHB][hapmap];0.90[CHD][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1014601	chr3:59666609-59888166	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA miRNA target site	1 gene(s)	inside rSNPs	diseases
2	nsv1003387	chr3:59756364-59831340	Enhancers Strong transcription Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	nsv460562	chr3:59760118-59826778	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv590381	chr3:59760118-59826778	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv590382	chr3:59763809-59793062	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS	n/a	n/a	inside rSNPs	diseases
6	nsv460563	chr3:59772342-59827390	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	nsv590383	chr3:59772342-59827390	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1905864	ID2B	cis	cerebellum	SCAN
rs1905864	IL17RD	cis	cerebellum	SCAN

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:59769800-59791400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
2	chr3:59770400-59825200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
3	chr3:59776800-59787000	Weak transcription	Primary T cells from cord blood	blood
4	chr3:59777000-59781800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr3:59777000-59786800	Weak transcription	Primary T helper cells fromperipheralblood	blood
6	chr3:59777200-59790800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
7	chr3:59777400-59785000	Weak transcription	Dnd41	blood
8	chr3:59778200-59811200	Weak transcription	Primary T helper cells PMA-I stimulated	--
9	chr3:59778400-59784400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr3:59778600-59782600	Enhancers	Fetal Thymus	thymus
11	chr3:59780400-59781600	Weak transcription	HSMMtube	muscle
12	chr3:59781200-59781600	Weak transcription	Thymus	Thymus

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links