Variant report

Variant	rs543923
Chromosome Location	chr11:104814286-104814287
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 44 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10128607	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10750715	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10791738	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10791740	1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2851169	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4522140	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs478674	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs478733	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs514537	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs520173	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs545491	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs547584	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs548182	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs553383	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs558960	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs569649	0.90[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs603840	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs617679	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs618197	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs632806	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs648421	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6591104	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs660576	0.86[CEU][hapmap];0.81[JPT][hapmap];0.87[EUR][1000 genomes]
rs675012	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs675358	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7104517	1.00[CEU][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7105050	0.95[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7127378	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7926199	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9326348	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs949154	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 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	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
3	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
4	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
5	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
6	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
7	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
8	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
9	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
10	nsv1041081	chr11:104797775-104912458	Strong transcription Enhancers Active TSS Weak transcription ZNF genes & repeats 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	5 gene(s)	inside rSNPs	diseases
11	nsv975395	chr11:104809055-104814705	Weak transcription Strong transcription Genic enhancers Enhancers	lncRNA	n/a	inside rSNPs	diseases
12	nsv1044970	chr11:104809246-105225032	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers 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	13 gene(s)	inside rSNPs	diseases
13	nsv541160	chr11:104809246-105225032	Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers Strong transcription 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	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs543923	CASP4	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:104803400-104819000	Weak transcription	Psoas Muscle	Psoas
2	chr11:104805600-104814800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr11:104805600-104814800	Weak transcription	Fetal Thymus	thymus
4	chr11:104806200-104814400	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr11:104806200-104814800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
6	chr11:104806400-104818200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr11:104806800-104814800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
8	chr11:104807000-104817800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
9	chr11:104807000-104818200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
10	chr11:104807200-104818000	Weak transcription	Left Ventricle	heart
11	chr11:104811400-104818800	Weak transcription	Small Intestine	intestine
12	chr11:104811600-104814800	Weak transcription	NHDF-Ad	bronchial
13	chr11:104811600-104815600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr11:104811800-104815400	Weak transcription	NHEK	skin
15	chr11:104812000-104814400	Weak transcription	Fetal Muscle Leg	muscle
16	chr11:104812000-104814800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr11:104812000-104825200	Strong transcription	Primary neutrophils fromperipheralblood	blood
18	chr11:104812200-104814600	Weak transcription	Osteobl	bone
19	chr11:104812200-104814800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
20	chr11:104812200-104816600	Weak transcription	Fetal Intestine Small	intestine
21	chr11:104812200-104819000	Weak transcription	Rectal Mucosa Donor 31	rectum
22	chr11:104812400-104819000	Weak transcription	Aorta	Aorta
23	chr11:104812600-104817800	Strong transcription	Monocytes-CD14+_RO01746	blood
24	chr11:104812600-104819200	Weak transcription	Gastric	stomach
25	chr11:104812600-104825600	Strong transcription	Placenta	Placenta
26	chr11:104812600-104826800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
27	chr11:104812800-104814400	Weak transcription	HMEC	breast
28	chr11:104812800-104814600	Weak transcription	HSMM	muscle
29	chr11:104812800-104816000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr11:104812800-104817400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr11:104812800-104821600	Weak transcription	Colonic Mucosa	Colon
32	chr11:104812800-104825600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr11:104812800-104825600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr11:104812800-104825600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr11:104812800-104825600	Strong transcription	Primary T helper cells fromperipheralblood	blood
36	chr11:104812800-104826200	Strong transcription	Primary T cells fromperipheralblood	blood
37	chr11:104812800-104826600	Strong transcription	Primary hematopoietic stem cells	blood
38	chr11:104812800-104829200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr11:104812800-104831800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr11:104813000-104814400	Strong transcription	Liver	Liver
41	chr11:104813000-104814800	Weak transcription	Fetal Muscle Trunk	muscle
42	chr11:104813000-104817800	Strong transcription	Primary B cells from peripheral blood	blood
43	chr11:104813000-104820400	Weak transcription	Stomach Smooth Muscle	stomach
44	chr11:104813000-104825400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
45	chr11:104813000-104825600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr11:104813000-104825800	Strong transcription	Dnd41	blood
47	chr11:104813200-104815800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr11:104813200-104815800	Strong transcription	Fetal Lung	lung
49	chr11:104813200-104817000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
50	chr11:104813200-104817800	Strong transcription	Primary monocytes fromperipheralblood	blood

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