Variant report

Variant	rs11225170
Chromosome Location	chr11:102093464-102093465
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 64 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10895272	0.95[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.81[TSI][hapmap];0.83[YRI][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10895273	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10895274	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10895275	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10895276	0.95[CEU][hapmap];0.86[JPT][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10895277	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.81[GIH][hapmap];0.91[JPT][hapmap];0.95[MEX][hapmap];0.86[TSI][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10895278	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10895280	0.93[ASN][1000 genomes]
rs10895282	0.82[ASN][1000 genomes]
rs11225156	0.90[CEU][hapmap];0.82[CHB][hapmap];0.85[EUR][1000 genomes]
rs11225160	0.86[CEU][hapmap];0.86[CHB][hapmap];0.81[EUR][1000 genomes]
rs11225163	0.85[CEU][hapmap];0.90[JPT][hapmap];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11225165	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11225167	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11225169	0.90[MEX][hapmap]
rs11225174	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11225177	0.94[ASN][1000 genomes]
rs11602707	0.85[CHB][hapmap];0.95[JPT][hapmap];0.84[MEX][hapmap]
rs11605954	0.86[CEU][hapmap];0.82[CHB][hapmap];0.93[TSI][hapmap];0.82[EUR][1000 genomes]
rs11608234	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12223991	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12226331	0.86[CEU][hapmap];0.95[JPT][hapmap];0.85[MEX][hapmap];0.91[TSI][hapmap];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12420287	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12421242	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12786272	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12787996	0.91[CEU][hapmap];0.86[CHB][hapmap];0.84[EUR][1000 genomes]
rs12790399	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12795624	0.90[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12807220	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17097475	0.90[CHB][hapmap];0.91[JPT][hapmap];0.80[ASN][1000 genomes]
rs17097547	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17097560	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1820455	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1893498	0.86[CEU][hapmap];0.86[CHB][hapmap];0.93[TSI][hapmap];0.83[EUR][1000 genomes]
rs2187525	0.86[CEU][hapmap];0.82[CHB][hapmap];0.93[TSI][hapmap];0.81[EUR][1000 genomes]
rs2282652	0.91[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.83[YRI][hapmap];0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2846836	0.81[MEX][hapmap]
rs3858420	0.95[CEU][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4447144	0.86[CEU][hapmap];0.82[CHB][hapmap];0.82[EUR][1000 genomes]
rs4475891	0.95[CEU][hapmap];0.90[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4754041	0.82[EUR][1000 genomes]
rs57027482	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs58751289	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61280272	0.88[ASN][1000 genomes]
rs7106107	0.81[MEX][hapmap]
rs7107909	0.85[MEX][hapmap]
rs7110355	0.85[MEX][hapmap]
rs7110557	0.86[CEU][hapmap];0.90[JPT][hapmap];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7112802	0.92[ASN][1000 genomes]
rs7120067	0.82[CEU][hapmap];0.90[CHB][hapmap];0.91[JPT][hapmap];0.95[MEX][hapmap];0.86[TSI][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7122907	0.95[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.90[GIH][hapmap];0.95[JPT][hapmap];0.93[TSI][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7124247	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs718891	0.93[ASN][1000 genomes]
rs7931576	0.95[CEU][hapmap];0.95[JPT][hapmap];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7942061	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8504	0.95[CEU][hapmap];0.81[GIH][hapmap];0.81[JPT][hapmap];0.95[MEX][hapmap];0.86[TSI][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11225170	CASP1	cis	parietal	SCAN

Chromatin state (count:82 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:102043800-102100400	Weak transcription	Pancreas	Pancrea
2	chr11:102059600-102100400	Weak transcription	Gastric	stomach
3	chr11:102062800-102096400	Weak transcription	Small Intestine	intestine
4	chr11:102063800-102096600	Weak transcription	Stomach Mucosa	stomach
5	chr11:102064000-102094400	Weak transcription	Duodenum Mucosa	Duodenum
6	chr11:102064000-102105400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr11:102071400-102094400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr11:102074000-102097000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr11:102074000-102104200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr11:102075400-102105600	Weak transcription	Rectal Smooth Muscle	rectum
11	chr11:102076200-102102200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr11:102077000-102097400	Weak transcription	Psoas Muscle	Psoas
13	chr11:102077600-102094400	Weak transcription	Stomach Smooth Muscle	stomach
14	chr11:102077600-102096600	Weak transcription	Esophagus	oesophagus
15	chr11:102077600-102096600	Weak transcription	Right Ventricle	heart
16	chr11:102078800-102096600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr11:102078800-102105600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr11:102079000-102094400	Weak transcription	Rectal Mucosa Donor 29	rectum
19	chr11:102079000-102107200	Weak transcription	Fetal Brain Male	brain
20	chr11:102080000-102094400	Weak transcription	Skeletal Muscle Female	skeletal muscle
21	chr11:102080800-102096400	Weak transcription	HSMMtube	muscle
22	chr11:102080800-102099600	Weak transcription	Colon Smooth Muscle	Colon
23	chr11:102081000-102096600	Weak transcription	H1 Cell Line	embryonic stem cell
24	chr11:102081000-102100000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr11:102081200-102118600	Weak transcription	H9 Cell Line	embryonic stem cell
26	chr11:102081400-102094600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr11:102081400-102096400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
28	chr11:102081400-102097800	Weak transcription	Cortex derived primary cultured neurospheres	brain
29	chr11:102085000-102096800	Weak transcription	Placenta Amnion	Placenta Amnion
30	chr11:102085200-102094400	Weak transcription	A549	lung
31	chr11:102085600-102096200	Strong transcription	Hela-S3	cervix
32	chr11:102086200-102094400	Weak transcription	HUES6 Cell Line	embryonic stem cell
33	chr11:102086200-102094400	Weak transcription	Liver	Liver
34	chr11:102086800-102096400	Weak transcription	Fetal Stomach	stomach
35	chr11:102086800-102111600	Weak transcription	Lung	lung
36	chr11:102087000-102094400	Weak transcription	Fetal Heart	heart
37	chr11:102088000-102094400	Weak transcription	Duodenum Smooth Muscle	Duodenum
38	chr11:102088400-102094200	Weak transcription	Adipose Nuclei	Adipose
39	chr11:102088600-102105200	Weak transcription	Brain Substantia Nigra	brain
40	chr11:102088800-102094200	Weak transcription	Fetal Muscle Leg	muscle
41	chr11:102088800-102096600	Weak transcription	Left Ventricle	heart
42	chr11:102089200-102094200	Weak transcription	HUES48 Cell Line	embryonic stem cell
43	chr11:102089200-102097800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr11:102090000-102094400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
45	chr11:102090600-102098000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr11:102091800-102095800	Strong transcription	HSMM	muscle
47	chr11:102091800-102102800	Weak transcription	Skeletal Muscle Male	skeletal muscle
48	chr11:102092000-102093600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr11:102092000-102093800	Strong transcription	Fetal Intestine Small	intestine
50	chr11:102092000-102093800	Genic enhancers	HMEC	breast

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