Variant report

Variant	rs650940
Chromosome Location	chr11:104768909-104768910
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 41 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10895740	0.84[EUR][1000 genomes]
rs10895744	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11226546	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11226547	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11226548	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11226549	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11226550	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11825902	0.94[EUR][1000 genomes]
rs12422201	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs15684	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17103153	0.84[EUR][1000 genomes]
rs2005513	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs478650	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs491011	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs491945	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs518553	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs524060	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs528641	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs532705	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs532738	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs548968	0.86[EUR][1000 genomes]
rs549691	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs573894	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs579156	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs595395	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs625046	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs626771	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs641046	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs656251	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs693312	0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 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	nsv1040536	chr11:104757419-104781022	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a
9	esv20820	chr11:104757749-104781659	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a
10	nsv556217	chr11:104758035-104781313	Enhancers Weak transcription ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a
11	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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs650940	CASP1	Cis_1M	lymphoblastoid	RTeQTL
rs650940	CASP1///COP1	Cis_1M	lymphoblastoid	RTeQTL
rs650940	CASP4	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:104763800-104769000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr11:104764800-104769000	Weak transcription	NHLF	lung
3	chr11:104765600-104769800	Active TSS	Aorta	Aorta
4	chr11:104766400-104769200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
5	chr11:104766600-104769200	Weak transcription	HUES48 Cell Line	embryonic stem cell
6	chr11:104766600-104769400	Weak transcription	HUES64 Cell Line	embryonic stem cell
7	chr11:104767000-104769200	Weak transcription	Fetal Stomach	stomach
8	chr11:104767800-104769600	Active TSS	Ovary	ovary
9	chr11:104768000-104769400	Active TSS	Rectal Mucosa Donor 29	rectum
10	chr11:104768200-104769200	Enhancers	Primary T cells fromperipheralblood	blood
11	chr11:104768200-104769400	Active TSS	Colon Smooth Muscle	Colon
12	chr11:104768200-104769400	Active TSS	Duodenum Smooth Muscle	Duodenum
13	chr11:104768200-104769400	Active TSS	Pancreatic Islets	Pancreatic Islet
14	chr11:104768200-104769600	Enhancers	Primary T killer memory cells from peripheral blood	blood
15	chr11:104768200-104769600	Active TSS	Stomach Smooth Muscle	stomach
16	chr11:104768200-104769800	Enhancers	Primary T helper cells fromperipheralblood	blood
17	chr11:104768400-104769000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr11:104768400-104769400	Active TSS	Brain Anterior Caudate	brain
19	chr11:104768400-104769400	Active TSS	Duodenum Mucosa	Duodenum
20	chr11:104768400-104769400	Active TSS	Rectal Mucosa Donor 31	rectum
21	chr11:104768400-104769400	Active TSS	Skeletal Muscle Female	skeletal muscle
22	chr11:104768400-104769600	Active TSS	Rectal Smooth Muscle	rectum
23	chr11:104768400-104769600	Active TSS	Right Atrium	heart
24	chr11:104768400-104770400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
25	chr11:104768600-104769000	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
26	chr11:104768600-104769000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
27	chr11:104768600-104769000	Active TSS	Primary T helper cells PMA-I stimulated	--
28	chr11:104768600-104769000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr11:104768600-104769000	Active TSS	Brain Hippocampus Middle	brain
30	chr11:104768600-104769200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr11:104768600-104769200	Enhancers	Primary T cells from cord blood	blood
32	chr11:104768600-104769200	Active TSS	Primary T helper 17 cells PMA-I stimulated	--
33	chr11:104768600-104769200	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr11:104768600-104769200	Active TSS	Brain Inferior Temporal Lobe	brain
35	chr11:104768600-104769200	Active TSS	Colonic Mucosa	Colon
36	chr11:104768600-104769200	Active TSS	Esophagus	oesophagus
37	chr11:104768600-104769200	Enhancers	Fetal Muscle Leg	muscle
38	chr11:104768600-104769200	Active TSS	Left Ventricle	heart
39	chr11:104768600-104769200	Active TSS	Lung	lung
40	chr11:104768600-104769200	Active TSS	Pancreas	Pancrea
41	chr11:104768600-104769400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
42	chr11:104768600-104769400	Active TSS	Skeletal Muscle Male	skeletal muscle
43	chr11:104768600-104769400	Flanking Active TSS	GM12878-XiMat	blood
44	chr11:104768600-104769400	Flanking Active TSS	HUVEC	blood vessel
45	chr11:104768600-104770200	Enhancers	Primary B cells from peripheral blood	blood
46	chr11:104768800-104769000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr11:104768800-104769000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
48	chr11:104768800-104769000	Active TSS	Adipose Nuclei	Adipose
49	chr11:104768800-104769000	Active TSS	NHDF-Ad	bronchial
50	chr11:104768800-104769200	Active TSS	Primary T regulatory cells fromperipheralblood	blood

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