Variant report

Variant	rs11130734
Chromosome Location	chr3:59784509-59784510
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 29 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs1352022	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1905864	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]
rs1905865	0.95[CHB][hapmap];0.84[JPT][hapmap];0.85[AFR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2046454	0.87[ASN][1000 genomes]
rs2629878	0.87[ASN][1000 genomes]
rs2629879	0.88[ASN][1000 genomes]
rs2629881	0.87[ASN][1000 genomes]
rs2629891	0.87[ASN][1000 genomes]
rs34764324	0.85[ASN][1000 genomes]
rs4455289	0.97[ASN][1000 genomes]
rs562516	0.95[CHB][hapmap];0.90[CHD][hapmap];0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs565226	0.90[JPT][hapmap]
rs606415	0.88[ASN][1000 genomes]
rs66805688	0.86[ASN][1000 genomes]
rs670592	0.95[JPT][hapmap]
rs67367323	0.87[ASN][1000 genomes]
rs6774343	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs67777617	0.83[ASN][1000 genomes]
rs6781354	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs683809	0.88[ASN][1000 genomes]
rs9311726	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.99[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	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
8	nsv428085	chr3:59782509-60070116	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11130734	ID2B	cis	cerebellum	SCAN
rs11130734	IL17RD	cis	cerebellum	SCAN

Chromatin state (count:15 , 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	chr3:59777000-59786800	Weak transcription	Primary T helper cells fromperipheralblood	blood
5	chr3:59777200-59790800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
6	chr3:59777400-59785000	Weak transcription	Dnd41	blood
7	chr3:59778200-59811200	Weak transcription	Primary T helper cells PMA-I stimulated	--
8	chr3:59782200-59785000	Weak transcription	Thymus	Thymus
9	chr3:59782400-59786400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr3:59782400-59794800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr3:59783600-59785600	Enhancers	HepG2	liver
12	chr3:59783800-59786000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
13	chr3:59784200-59784800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr3:59784200-59787800	Enhancers	Fetal Thymus	thymus
15	chr3:59784400-59785200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links