Variant report

Variant	rs10895280
Chromosome Location	chr11:102108422-102108423
allele	A/C/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 65 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10791570	0.87[EUR][1000 genomes]
rs10895272	0.86[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];0.86[JPT][hapmap];0.90[MEX][hapmap];0.93[ASN][1000 genomes]
rs10895273	0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10895274	0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10895275	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10895276	0.86[CEU][hapmap];0.95[JPT][hapmap];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10895277	0.86[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.96[MKK][hapmap];0.81[TSI][hapmap];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10895278	0.86[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10895282	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10895283	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11225156	0.82[CEU][hapmap];0.82[CHB][hapmap]
rs11225160	0.87[CEU][hapmap];0.86[CHB][hapmap]
rs11225163	0.85[CEU][hapmap];0.85[JPT][hapmap]
rs11225165	0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11225167	0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11225169	0.80[MEX][hapmap]
rs11225170	0.82[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.91[JPT][hapmap];0.90[MEX][hapmap];0.93[ASN][1000 genomes]
rs11225174	0.86[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11225177	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11602707	0.85[CHB][hapmap];0.86[JPT][hapmap]
rs11605954	0.87[CEU][hapmap];0.82[CHB][hapmap]
rs11608234	0.91[ASN][1000 genomes]
rs12223991	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12226331	0.87[CEU][hapmap];0.87[JPT][hapmap];0.95[MEX][hapmap]
rs12420287	0.91[ASN][1000 genomes]
rs12421242	0.91[ASN][1000 genomes]
rs12786272	0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12787996	0.82[CEU][hapmap];0.86[CHB][hapmap]
rs12790399	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12795624	0.91[CEU][hapmap];0.90[CHB][hapmap];0.90[JPT][hapmap];0.92[ASN][1000 genomes]
rs12807220	0.95[ASN][1000 genomes]
rs17097475	0.90[CHB][hapmap];0.82[JPT][hapmap]
rs17097547	0.86[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17097560	0.86[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1820455	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1893498	0.87[CEU][hapmap];0.86[CHB][hapmap]
rs2187525	0.87[CEU][hapmap];0.82[CHB][hapmap]
rs2282652	0.85[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.91[JPT][hapmap];0.95[MEX][hapmap];0.91[MKK][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2846836	0.90[MEX][hapmap]
rs3858420	0.86[CEU][hapmap];0.87[JPT][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4447144	0.87[CEU][hapmap];0.82[CHB][hapmap]
rs4475891	0.86[CEU][hapmap];0.87[JPT][hapmap];0.95[MEX][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs57027482	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs58751289	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs60306966	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs61280272	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7106107	0.81[MEX][hapmap]
rs7110355	0.85[MEX][hapmap]
rs7110557	0.87[CEU][hapmap];0.81[JPT][hapmap]
rs7112802	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7120067	0.82[CEU][hapmap];0.90[CHB][hapmap];0.81[JPT][hapmap];0.85[MEX][hapmap]
rs7122907	0.86[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.86[JPT][hapmap];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7124247	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs718891	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7931576	0.86[CEU][hapmap];0.87[JPT][hapmap];0.81[ASN][1000 genomes]
rs7942061	0.86[ASN][1000 genomes]
rs8504	0.86[CEU][hapmap];0.91[JPT][hapmap];0.95[MEX][hapmap];0.81[TSI][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[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	esv3362945	chr11:101736547-102114246	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
2	nsv1052348	chr11:101987090-102255753	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
3	nsv556141	chr11:101988061-102207851	Weak transcription Genic enhancers Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv1050961	chr11:101993880-102253717	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
5	nsv1051735	chr11:101993880-102255753	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
6	nsv530646	chr11:102000840-102238992	Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
7	nsv832251	chr11:102012295-102181744	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
8	nsv1043388	chr11:102017719-102172857	Genic enhancers Enhancers Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10895280	CASP1	cis	parietal	SCAN
rs10895280	CASP5	cis	parietal	SCAN

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:102081200-102118600	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr11:102086800-102111600	Weak transcription	Lung	lung
3	chr11:102093000-102113000	Weak transcription	Ovary	ovary
4	chr11:102095200-102118600	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr11:102096800-102114600	Weak transcription	Small Intestine	intestine
6	chr11:102097800-102119600	Weak transcription	Right Atrium	heart
7	chr11:102098000-102111600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr11:102098400-102118600	Weak transcription	Rectal Mucosa Donor 29	rectum
9	chr11:102099000-102112800	Weak transcription	Hela-S3	cervix
10	chr11:102100800-102109000	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr11:102100800-102111400	Weak transcription	A549	lung
12	chr11:102100800-102112800	Weak transcription	Fetal Heart	heart
13	chr11:102100800-102113000	Weak transcription	Esophagus	oesophagus
14	chr11:102101000-102111200	Weak transcription	NHLF	lung
15	chr11:102101200-102108800	Weak transcription	Fetal Intestine Large	intestine
16	chr11:102101800-102112800	Weak transcription	Liver	Liver
17	chr11:102102000-102115400	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr11:102102200-102111600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr11:102104600-102118600	Weak transcription	Fetal Muscle Trunk	muscle
20	chr11:102105000-102118600	Weak transcription	Duodenum Smooth Muscle	Duodenum
21	chr11:102105200-102109000	Weak transcription	Fetal Intestine Small	intestine
22	chr11:102105200-102118600	Weak transcription	Fetal Muscle Leg	muscle
23	chr11:102105200-102118600	Weak transcription	Fetal Stomach	stomach
24	chr11:102105200-102118600	Weak transcription	Left Ventricle	heart
25	chr11:102105400-102111400	Weak transcription	Fetal Lung	lung
26	chr11:102105400-102112000	Weak transcription	Cortex derived primary cultured neurospheres	brain
27	chr11:102105400-102115400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr11:102105600-102110000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr11:102105600-102110000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr11:102105800-102111200	Weak transcription	NHDF-Ad	bronchial
31	chr11:102106000-102108800	Weak transcription	Stomach Smooth Muscle	stomach
32	chr11:102106000-102109400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
33	chr11:102106000-102111400	Weak transcription	NH-A	brain
34	chr11:102106000-102112000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr11:102106000-102113200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr11:102106000-102115800	Weak transcription	Aorta	Aorta
37	chr11:102106000-102118600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr11:102106200-102111400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr11:102106200-102112800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
40	chr11:102106200-102118600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
41	chr11:102106200-102118600	Weak transcription	Skeletal Muscle Female	skeletal muscle
42	chr11:102106400-102118600	Weak transcription	HUES6 Cell Line	embryonic stem cell
43	chr11:102107200-102108600	Enhancers	HMEC	breast
44	chr11:102107200-102109200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr11:102107400-102108600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr11:102107400-102108600	Enhancers	HSMM	muscle
47	chr11:102107400-102109200	Enhancers	HepG2	liver
48	chr11:102107400-102109600	Enhancers	Adipose Nuclei	Adipose
49	chr11:102107800-102108600	Enhancers	ES-I3 Cell Line	embryonic stem cell
50	chr11:102107800-102109400	Enhancers	Fetal Kidney	kidney

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