Variant report

Variant	rs520173
Chromosome Location	chr11:104788061-104788062
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 46 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10128607	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10750715	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10791738	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10791740	0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2851169	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4522140	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs478674	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs478733	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs514537	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs543923	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs545491	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs547584	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs548182	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs553383	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs558960	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs569649	0.90[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs603840	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs617679	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs618197	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs632806	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs648421	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6591104	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs660576	0.87[CEU][hapmap];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs675012	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs675358	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7104517	1.00[CEU][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7105050	0.95[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7127378	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7926199	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9326348	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs949154	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1046098	chr11:104207210-105003661	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv1054456	chr11:104358924-104805251	Weak transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv531430	chr11:104380924-105194452	Genic enhancers Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
4	nsv832255	chr11:104674918-104846961	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
5	esv2757474	chr11:104719593-104798545	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	esv2759862	chr11:104719593-104798545	Active TSS Enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	nsv898355	chr11:104730322-104897843	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
8	nsv1040784	chr11:104763797-104855878	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
9	nsv468862	chr11:104774014-105243371	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers 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	15 gene(s)	inside rSNPs	diseases
10	nsv556218	chr11:104774014-105243371	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Genic enhancers 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	15 gene(s)	inside rSNPs	diseases
11	esv3334824	chr11:104776753-104813836	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island lncRNA	1 gene(s)	inside rSNPs	diseases
12	nsv898356	chr11:104779195-104838471	Enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
13	esv3385159	chr11:104786549-105051555	Strong transcription Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
14	esv3356969	chr11:104786594-104803934	Enhancers Flanking Active TSS Weak transcription Active TSS	TF binding region CpG island lncRNA	1 gene(s)	inside rSNPs	diseases
15	nsv983232	chr11:104787454-104809055	Flanking Active TSS Enhancers Active TSS Weak transcription	TF binding region CpG island lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs520173	CASP4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:104778400-104788800	Weak transcription	Pancreas	Pancrea
2	chr11:104786600-104788200	Enhancers	Primary T cells from cord blood	blood
3	chr11:104786800-104789400	Flanking Active TSS	HUVEC	blood vessel
4	chr11:104786800-104789800	Active TSS	Aorta	Aorta
5	chr11:104787000-104788200	Weak transcription	Skeletal Muscle Male	skeletal muscle
6	chr11:104787000-104788600	Weak transcription	Left Ventricle	heart
7	chr11:104787000-104788600	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr11:104787000-104788600	Weak transcription	Small Intestine	intestine
9	chr11:104787000-104789200	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr11:104787000-104789400	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
11	chr11:104787000-104789600	Active TSS	Primary T cells fromperipheralblood	blood
12	chr11:104787000-104789600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
13	chr11:104787200-104788200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr11:104787200-104788400	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
15	chr11:104787200-104788400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr11:104787200-104789400	Active TSS	Ovary	ovary
17	chr11:104787200-104789600	Active TSS	Duodenum Mucosa	Duodenum
18	chr11:104787400-104788200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
19	chr11:104787400-104788200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr11:104787400-104788200	Enhancers	Colon Smooth Muscle	Colon
21	chr11:104787400-104788400	Enhancers	Primary B cells from cord blood	blood
22	chr11:104787400-104789400	Active TSS	Stomach Smooth Muscle	stomach
23	chr11:104787400-104789600	Active TSS	Rectal Mucosa Donor 29	rectum
24	chr11:104787400-104789600	Active TSS	Right Atrium	heart
25	chr11:104787600-104788400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr11:104787600-104788400	Weak transcription	GM12878-XiMat	blood
27	chr11:104787600-104789200	Active TSS	Duodenum Smooth Muscle	Duodenum
28	chr11:104787600-104789200	Active TSS	Fetal Muscle Leg	muscle
29	chr11:104787600-104789400	Active TSS	Psoas Muscle	Psoas
30	chr11:104787800-104788200	Flanking Active TSS	Rectal Smooth Muscle	rectum
31	chr11:104787800-104788400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
32	chr11:104787800-104789000	Active TSS	Fetal Lung	lung
33	chr11:104787800-104789200	Active TSS	Primary T helper naive cells from peripheral blood	blood
34	chr11:104787800-104789200	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
35	chr11:104787800-104789400	Active TSS	Breast Myoepithelial Primary Cells	Breast
36	chr11:104787800-104789400	Active TSS	NHDF-Ad	bronchial
37	chr11:104787800-104789600	Flanking Active TSS	Dnd41	blood
38	chr11:104788000-104788200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr11:104788000-104788200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
40	chr11:104788000-104788200	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
41	chr11:104788000-104788200	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
42	chr11:104788000-104788200	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
43	chr11:104788000-104788200	Flanking Active TSS	Fetal Stomach	stomach
44	chr11:104788000-104788200	Flanking Active TSS	NHLF	lung
45	chr11:104788000-104788400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr11:104788000-104788400	Flanking Active TSS	Primary B cells from peripheral blood	blood
47	chr11:104788000-104788400	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
48	chr11:104788000-104788400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr11:104788000-104788400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr11:104788000-104788400	Flanking Active TSS	Adipose Nuclei	Adipose

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