Variant report

Variant	rs11605954
Chromosome Location	chr11:102049221-102049222
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 58 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10895269	0.84[MEX][hapmap]
rs10895272	0.91[CEU][hapmap];0.82[CHB][hapmap];0.88[TSI][hapmap];0.83[EUR][1000 genomes]
rs10895273	0.86[EUR][1000 genomes]
rs10895274	0.86[EUR][1000 genomes]
rs10895275	0.86[EUR][1000 genomes]
rs10895276	0.91[CEU][hapmap];0.86[EUR][1000 genomes]
rs10895277	0.91[CEU][hapmap];0.82[CHB][hapmap];0.93[TSI][hapmap];0.86[EUR][1000 genomes]
rs10895278	0.91[CEU][hapmap];0.82[CHB][hapmap];0.84[EUR][1000 genomes]
rs11225156	0.95[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11225160	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11225163	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs11225165	0.86[EUR][1000 genomes]
rs11225167	0.87[EUR][1000 genomes]
rs11225170	0.86[CEU][hapmap];0.82[CHB][hapmap];0.93[TSI][hapmap];0.82[EUR][1000 genomes]
rs11225174	0.91[CEU][hapmap];0.82[CHB][hapmap];0.83[EUR][1000 genomes]
rs11608234	0.81[EUR][1000 genomes]
rs12223991	0.83[EUR][1000 genomes]
rs12226331	1.00[CEU][hapmap];0.92[GIH][hapmap];0.98[TSI][hapmap];0.92[EUR][1000 genomes]
rs12420287	0.94[EUR][1000 genomes]
rs12421242	0.93[EUR][1000 genomes]
rs12786272	0.87[EUR][1000 genomes]
rs12787996	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12790399	0.84[EUR][1000 genomes]
rs12793501	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12795624	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs17097547	0.91[CEU][hapmap];0.82[CHB][hapmap];0.84[EUR][1000 genomes]
rs17097560	0.91[CEU][hapmap];0.82[CHB][hapmap];0.84[EUR][1000 genomes]
rs1820455	0.87[EUR][1000 genomes]
rs1893498	1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1942683	0.83[MEX][hapmap]
rs2187525	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2282652	0.91[CEU][hapmap];0.82[CHB][hapmap];0.87[GIH][hapmap];1.00[TSI][hapmap];0.83[EUR][1000 genomes]
rs3858420	0.91[CEU][hapmap];0.84[EUR][1000 genomes]
rs4420227	0.92[MEX][hapmap]
rs4447144	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4475891	0.91[CEU][hapmap];0.88[GIH][hapmap];1.00[TSI][hapmap];0.83[EUR][1000 genomes]
rs4561174	0.92[MEX][hapmap]
rs4754041	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4754833	0.87[GIH][hapmap]
rs57027482	0.81[EUR][1000 genomes]
rs58751289	0.83[EUR][1000 genomes]
rs7110557	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs7120067	0.95[CEU][hapmap];0.92[GIH][hapmap];0.93[TSI][hapmap];0.88[EUR][1000 genomes]
rs7122907	0.91[CEU][hapmap];0.82[CHB][hapmap];0.90[GIH][hapmap];1.00[TSI][hapmap];0.87[EUR][1000 genomes]
rs7124247	0.83[EUR][1000 genomes]
rs7931576	0.91[CEU][hapmap];0.85[EUR][1000 genomes]
rs7942061	0.87[EUR][1000 genomes]
rs8504	0.91[CEU][hapmap];0.93[TSI][hapmap];0.83[EUR][1000 genomes]
rs948737	0.87[GIH][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 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
8	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
9	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
rs11605954	CASP1	cis	parietal	SCAN
rs11605954	C11orf70	cis	parietal	SCAN

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:102026400-102059400	Weak transcription	Fetal Brain Male	brain
2	chr11:102028000-102062800	Weak transcription	Duodenum Mucosa	Duodenum
3	chr11:102028600-102055200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr11:102029200-102067600	Weak transcription	HSMMtube	muscle
5	chr11:102029400-102050000	Weak transcription	Skeletal Muscle Male	skeletal muscle
6	chr11:102033400-102061000	Weak transcription	Right Ventricle	heart
7	chr11:102034400-102055200	Weak transcription	Cortex derived primary cultured neurospheres	brain
8	chr11:102034400-102057200	Weak transcription	H1 Cell Line	embryonic stem cell
9	chr11:102034600-102076800	Weak transcription	Rectal Mucosa Donor 29	rectum
10	chr11:102035400-102055600	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr11:102036000-102069400	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr11:102036200-102050200	Weak transcription	Fetal Intestine Small	intestine
13	chr11:102037400-102049800	Weak transcription	Fetal Heart	heart
14	chr11:102039600-102056800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr11:102041600-102062400	Weak transcription	Left Ventricle	heart
16	chr11:102042400-102050000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr11:102042400-102055400	Weak transcription	Colon Smooth Muscle	Colon
18	chr11:102042800-102049400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr11:102042800-102057200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr11:102043800-102051600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr11:102043800-102077000	Weak transcription	Esophagus	oesophagus
22	chr11:102043800-102100400	Weak transcription	Pancreas	Pancrea
23	chr11:102044000-102055200	Weak transcription	Gastric	stomach
24	chr11:102045800-102049600	Weak transcription	Fetal Muscle Leg	muscle
25	chr11:102045800-102050800	Weak transcription	Fetal Muscle Trunk	muscle
26	chr11:102046000-102055400	Weak transcription	Ovary	ovary
27	chr11:102046600-102049800	Weak transcription	Adipose Nuclei	Adipose
28	chr11:102046600-102056800	Weak transcription	HUES6 Cell Line	embryonic stem cell
29	chr11:102046600-102057000	Weak transcription	Fetal Kidney	kidney
30	chr11:102046800-102056800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
31	chr11:102046800-102076600	Weak transcription	Stomach Smooth Muscle	stomach
32	chr11:102047000-102057200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr11:102047600-102049400	Enhancers	Placenta	Placenta
34	chr11:102047600-102049600	Weak transcription	Fetal Stomach	stomach
35	chr11:102047600-102049600	Enhancers	NH-A	brain
36	chr11:102047600-102049800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr11:102047600-102050000	Enhancers	Muscle Satellite Cultured Cells	--
38	chr11:102047600-102050400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr11:102047600-102050600	Enhancers	HMEC	breast
40	chr11:102047800-102049800	Enhancers	HepG2	liver
41	chr11:102047800-102050000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr11:102047800-102050000	Enhancers	Placenta Amnion	Placenta Amnion
43	chr11:102047800-102050400	Enhancers	HUVEC	blood vessel
44	chr11:102048000-102055200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr11:102048200-102049400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
46	chr11:102048200-102050400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr11:102048200-102062400	Weak transcription	Liver	Liver
48	chr11:102048400-102049600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr11:102048400-102050200	Enhancers	Small Intestine	intestine
50	chr11:102048400-102065200	Weak transcription	Aorta	Aorta

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