Variant report

Variant	rs2003357
Chromosome Location	chr11:101999276-101999277
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:68)

rs_ID	r²[population]
rs10750632	0.87[ASN][1000 genomes]
rs10750633	0.82[CHB][hapmap];0.86[JPT][hapmap];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10750634	0.84[JPT][hapmap];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10791564	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10791565	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.89[YRI][hapmap];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10895256	0.82[MEX][hapmap]
rs10895258	0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10895259	0.87[ASN][1000 genomes]
rs10895261	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10895262	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10895263	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10895264	0.82[CHB][hapmap];0.86[JPT][hapmap];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10895265	0.82[ASN][1000 genomes]
rs10895266	1.00[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11225134	0.86[ASN][1000 genomes]
rs11225135	0.87[CHB][hapmap];0.87[JPT][hapmap];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11225139	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11225141	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11225146	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11225147	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11225149	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11225151	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11603468	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11606471	0.87[ASN][1000 genomes]
rs11607135	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12223094	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12790160	0.86[ASN][1000 genomes]
rs12796162	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1365330	0.81[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.91[TSI][hapmap];0.90[YRI][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1426392	0.83[CHB][hapmap];0.87[JPT][hapmap];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1426394	0.87[JPT][hapmap];0.82[ASN][1000 genomes]
rs1834595	0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1834596	0.83[CHB][hapmap];0.87[JPT][hapmap];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1893497	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1895917	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1942680	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1942688	0.87[ASN][1000 genomes]
rs1942689	0.87[CHB][hapmap];0.87[JPT][hapmap];0.87[ASN][1000 genomes]
rs1942690	0.87[ASN][1000 genomes]
rs1942691	0.81[ASN][1000 genomes]
rs2019070	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3890538	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]
rs4329661	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4442513	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4754833	0.87[JPT][hapmap];0.82[TSI][hapmap];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4754834	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs60304309	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61538959	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61918361	0.83[AFR][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];0.91[TSI][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7106388	0.82[MEX][hapmap]
rs7108698	0.81[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.98[TSI][hapmap];0.90[YRI][hapmap];0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7108820	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7117239	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7120363	0.81[ASN][1000 genomes]
rs7123862	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7124280	0.81[CHB][hapmap];0.86[JPT][hapmap];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7126535	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7127597	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7130772	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7483889	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7924449	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7924737	0.87[JPT][hapmap];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7927957	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7928547	0.87[CHB][hapmap];0.87[JPT][hapmap];0.87[ASN][1000 genomes]
rs7938172	0.96[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.88[TSI][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs948737	0.87[JPT][hapmap];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9787890	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2003357	CASP1	cis	parietal	SCAN

Chromatin state (count:78 , 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	chr11:101991600-102002200	Weak transcription	Colon Smooth Muscle	Colon
9	chr11:101991600-102006000	Weak transcription	NHLF	lung
10	chr11:101991600-102008800	Weak transcription	HSMMtube	muscle
11	chr11:101991600-102012400	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr11:101991600-102015200	Weak transcription	Fetal Kidney	kidney
13	chr11:101991600-102015600	Weak transcription	Duodenum Smooth Muscle	Duodenum
14	chr11:101991800-102001000	Weak transcription	HSMM	muscle
15	chr11:101991800-102001400	Strong transcription	Fetal Stomach	stomach
16	chr11:101992000-101999600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr11:101992600-102003600	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr11:101992800-102008800	Weak transcription	NHDF-Ad	bronchial
19	chr11:101993200-102000000	Weak transcription	Lung	lung
20	chr11:101993600-102000000	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr11:101995200-101999400	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
22	chr11:101995200-101999800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr11:101995400-101999800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr11:101995400-102002200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr11:101995800-102001000	Weak transcription	Fetal Lung	lung
26	chr11:101996000-102008000	Weak transcription	Esophagus	oesophagus
27	chr11:101996000-102009000	Weak transcription	Aorta	Aorta
28	chr11:101996200-101999400	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
29	chr11:101996800-102000600	Weak transcription	Right Atrium	heart
30	chr11:101997000-102006200	Weak transcription	Hela-S3	cervix
31	chr11:101997200-102001200	Weak transcription	NHEK	skin
32	chr11:101997200-102001600	Weak transcription	Fetal Heart	heart
33	chr11:101997200-102001600	Weak transcription	NH-A	brain
34	chr11:101997400-102002000	Weak transcription	Muscle Satellite Cultured Cells	--
35	chr11:101997600-102001600	Weak transcription	HMEC	breast
36	chr11:101997600-102004400	Weak transcription	Fetal Intestine Large	intestine
37	chr11:101997600-102009000	Weak transcription	A549	lung
38	chr11:101997600-102009000	Weak transcription	Osteobl	bone
39	chr11:101998000-101999400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr11:101998400-101999600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr11:101998400-102001200	Weak transcription	Adipose Nuclei	Adipose
42	chr11:101998400-102002000	Weak transcription	Right Ventricle	heart
43	chr11:101998400-102005400	Weak transcription	Left Ventricle	heart
44	chr11:101998400-102006000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
45	chr11:101998600-102000800	Weak transcription	Placenta Amnion	Placenta Amnion
46	chr11:101998600-102001200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr11:101998600-102001200	Weak transcription	Skeletal Muscle Male	skeletal muscle
48	chr11:101998600-102001600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr11:101998600-102001800	Weak transcription	Psoas Muscle	Psoas
50	chr11:101998600-102006000	Weak transcription	Gastric	stomach

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