Variant report

Variant	rs3890538
Chromosome Location	chr11:102006169-102006170
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 74 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs10750632	0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10750633	0.82[CHB][hapmap];0.86[JPT][hapmap];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10750634	0.85[CHB][hapmap];0.84[JPT][hapmap];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10791564	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10791565	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10895256	0.82[MEX][hapmap]
rs10895258	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10895259	0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10895261	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10895262	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10895263	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10895264	0.82[CHB][hapmap];0.86[JPT][hapmap];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10895265	0.84[ASN][1000 genomes]
rs10895266	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11225134	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11225135	0.87[JPT][hapmap];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11225139	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11225141	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11225146	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11225147	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11225149	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11225151	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11603468	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11606471	0.85[ASN][1000 genomes]
rs11607135	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12223094	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12790160	0.86[ASN][1000 genomes]
rs12796162	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1365330	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1426392	0.83[CHB][hapmap];0.87[JPT][hapmap];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1426394	0.87[CHB][hapmap];0.87[JPT][hapmap];0.84[ASN][1000 genomes]
rs1426395	0.84[AFR][1000 genomes]
rs1834595	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1834596	0.83[CHB][hapmap];0.87[JPT][hapmap];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1893497	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1895917	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1942680	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1942688	0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1942689	0.82[CHB][hapmap];0.87[JPT][hapmap];0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1942690	0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2003357	0.81[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.98[TSI][hapmap];0.90[YRI][hapmap];0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2019070	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4329661	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4442513	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4754833	0.87[CHB][hapmap];0.87[JPT][hapmap];0.84[TSI][hapmap];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4754834	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs60304309	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61538959	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61918361	0.90[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs6590949	1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.90[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7106388	0.82[MEX][hapmap]
rs7108698	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7108820	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7117239	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7123862	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7124280	0.81[CHB][hapmap];0.86[JPT][hapmap];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7126535	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7127597	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.90[YRI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7130772	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7483889	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.90[YRI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7924449	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7924737	0.87[CHB][hapmap];0.87[JPT][hapmap];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7927957	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7928547	0.87[JPT][hapmap];0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7938172	0.96[CEU][hapmap];0.91[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.88[TSI][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs948737	0.87[CHB][hapmap];0.87[JPT][hapmap];0.82[TSI][hapmap];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9787890	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[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	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	nsv898333	chr11:101832670-102079986	Active TSS Flanking Bivalent TSS/Enh Enhancers Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	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
4	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
5	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
6	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
7	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3890538	CASP1	cis	parietal	SCAN

Chromatin state (count:79 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:101983600-102014800	Weak transcription	Pancreas	Pancrea
2	chr11:101985200-102009200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr11:101988800-102009000	Weak transcription	Stomach Smooth Muscle	stomach
4	chr11:101988800-102009600	Weak transcription	Rectal Smooth Muscle	rectum
5	chr11:101989600-102015200	Weak transcription	Rectal Mucosa Donor 29	rectum
6	chr11:101991000-102009000	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr11:101991000-102010000	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr11:101991600-102008800	Weak transcription	HSMMtube	muscle
9	chr11:101991600-102012400	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr11:101991600-102015200	Weak transcription	Fetal Kidney	kidney
11	chr11:101991600-102015600	Weak transcription	Duodenum Smooth Muscle	Duodenum
12	chr11:101992800-102008800	Weak transcription	NHDF-Ad	bronchial
13	chr11:101996000-102008000	Weak transcription	Esophagus	oesophagus
14	chr11:101996000-102009000	Weak transcription	Aorta	Aorta
15	chr11:101997000-102006200	Weak transcription	Hela-S3	cervix
16	chr11:101997600-102009000	Weak transcription	A549	lung
17	chr11:101997600-102009000	Weak transcription	Osteobl	bone
18	chr11:101998600-102033000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr11:101998600-102034200	Weak transcription	Fetal Muscle Trunk	muscle
20	chr11:101998800-102008000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr11:101998800-102009200	Weak transcription	HUES48 Cell Line	embryonic stem cell
22	chr11:101998800-102009800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr11:101998800-102014400	Weak transcription	Liver	Liver
24	chr11:101998800-102014600	Weak transcription	Small Intestine	intestine
25	chr11:101998800-102014800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
26	chr11:101999000-102008800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr11:101999000-102008800	Weak transcription	Placenta	Placenta
28	chr11:101999000-102010000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr11:101999000-102012600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr11:101999400-102009200	Weak transcription	HUES64 Cell Line	embryonic stem cell
31	chr11:101999400-102010000	Weak transcription	H1 Cell Line	embryonic stem cell
32	chr11:101999600-102009400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr11:102000800-102007800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr11:102000800-102034000	Weak transcription	Lung	lung
35	chr11:102001200-102010000	Weak transcription	Placenta Amnion	Placenta Amnion
36	chr11:102001600-102007800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr11:102002000-102007600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr11:102002400-102008800	Weak transcription	NH-A	brain
39	chr11:102002400-102009000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr11:102002400-102009000	Weak transcription	Muscle Satellite Cultured Cells	--
41	chr11:102002400-102009600	Weak transcription	Duodenum Mucosa	Duodenum
42	chr11:102002400-102010000	Weak transcription	HUES6 Cell Line	embryonic stem cell
43	chr11:102002400-102010000	Weak transcription	Colon Smooth Muscle	Colon
44	chr11:102002400-102010200	Weak transcription	Brain Cingulate Gyrus	brain
45	chr11:102003600-102006200	Strong transcription	Fetal Stomach	stomach
46	chr11:102003600-102007400	Strong transcription	Fetal Intestine Small	intestine
47	chr11:102003600-102009600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr11:102003800-102008000	Strong transcription	HepG2	liver
49	chr11:102004400-102006200	Strong transcription	Fetal Intestine Large	intestine
50	chr11:102004400-102008600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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