Variant report

Variant	rs11229240
Chromosome Location	chr11:57825450-57825451
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 33 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10896705	0.82[LWK][hapmap]
rs11229216	1.00[CEU][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes]
rs11229225	0.91[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs11229228	0.91[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs11229229	0.91[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs11229232	0.91[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs11229238	1.00[CEU][hapmap];0.84[CHD][hapmap];0.81[MEX][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes]
rs11229246	1.00[ASW][hapmap];0.93[CEU][hapmap];0.86[GIH][hapmap];0.93[LWK][hapmap];0.80[MEX][hapmap];0.94[MKK][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11229251	0.86[CEU][hapmap];1.00[YRI][hapmap]
rs11229255	0.86[CEU][hapmap];0.84[CHD][hapmap];0.82[JPT][hapmap];0.92[TSI][hapmap]
rs12361813	0.88[AFR][1000 genomes]
rs12793317	0.86[CEU][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap]
rs1349481	1.00[YRI][hapmap]
rs1447173	1.00[JPT][hapmap];1.00[YRI][hapmap]
rs17459653	0.86[CEU][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap]
rs17537868	1.00[ASW][hapmap];1.00[CEU][hapmap];0.92[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.88[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2441956	0.82[CEU][hapmap];0.83[CHD][hapmap];0.89[TSI][hapmap]
rs2441971	0.87[EUR][1000 genomes]
rs2514205	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28650443	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs34216610	0.96[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs35157521	0.91[AFR][1000 genomes]
rs3844134	0.86[TSI][hapmap]
rs4938884	0.91[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs4939178	0.96[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4939179	0.86[CEU][hapmap];0.92[CHD][hapmap];0.82[JPT][hapmap];1.00[LWK][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4939185	0.82[JPT][hapmap];0.93[LWK][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs61738000	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[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	nsv1044030	chr11:57073395-58035564	Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
2	nsv541047	chr11:57073395-58035564	Active TSS Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
3	nsv1054205	chr11:57544264-58358509	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
4	nsv897589	chr11:57623815-58052357	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
5	nsv832165	chr11:57806024-58009076	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11229240	TIMM10	cis	parietal	SCAN
rs11229240	TIMM10	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:57821600-57826000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
2	chr11:57823600-57828400	Enhancers	HepG2	liver
3	chr11:57824600-57826400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr11:57824600-57830000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr11:57824600-57830600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr11:57824800-57825800	Enhancers	HSMM	muscle
7	chr11:57824800-57826000	Enhancers	HSMMtube	muscle
8	chr11:57824800-57826800	Enhancers	Breast Myoepithelial Primary Cells	Breast
9	chr11:57824800-57830000	Enhancers	Placenta Amnion	Placenta Amnion
10	chr11:57824800-57830200	Enhancers	NHLF	lung
11	chr11:57825000-57826400	Enhancers	Pancreas	Pancrea
12	chr11:57825000-57826800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr11:57825000-57826800	Enhancers	Placenta	Placenta
14	chr11:57825000-57830200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr11:57825000-57830600	Enhancers	HMEC	breast
16	chr11:57825200-57825800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr11:57825200-57826800	Enhancers	H1 Cell Line	embryonic stem cell
18	chr11:57825200-57830600	Enhancers	NHEK	skin
19	chr11:57825400-57826800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr11:57825400-57828800	Enhancers	Fetal Heart	heart
21	chr11:57825400-57830000	Enhancers	Muscle Satellite Cultured Cells	--

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