Variant report

Variant	rs648896
Chromosome Location	chr11:77551500-77551501
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 49 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10899404	0.81[EUR][1000 genomes]
rs11237280	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11237318	0.82[EUR][1000 genomes]
rs11600998	0.82[ASN][1000 genomes]
rs11603438	0.80[ASN][1000 genomes]
rs11604207	0.80[ASN][1000 genomes]
rs12285765	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1783544	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2154972	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs24356	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2508189	0.82[EUR][1000 genomes]
rs34130561	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4322421	0.81[EUR][1000 genomes]
rs484363	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4945220	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs537811	0.81[EUR][1000 genomes]
rs56218634	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs588217	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs598071	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs614495	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs621456	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs623173	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs623907	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs635195	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs636971	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs643388	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs648601	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs650171	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs663674	0.81[EUR][1000 genomes]
rs667225	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs668701	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs670090	0.80[EUR][1000 genomes]
rs684813	0.93[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs687037	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs694845	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs695046	0.82[EUR][1000 genomes]
rs7123080	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs72945598	0.86[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs72947625	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs72947668	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs72949616	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72949618	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7950873	0.86[AFR][1000 genomes]
rs7951033	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs947841	0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1050891	chr11:77416645-77788002	Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
2	nsv1037292	chr11:77431583-77745934	Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
3	nsv541092	chr11:77431583-77745934	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
4	nsv949316	chr11:77454076-77769885	Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs648896	INTS4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:70 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:77533000-77553800	Weak transcription	Brain Angular Gyrus	brain
2	chr11:77533000-77554000	Weak transcription	Brain Substantia Nigra	brain
3	chr11:77533000-77554200	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr11:77533400-77552200	Weak transcription	Brain Hippocampus Middle	brain
5	chr11:77533400-77552200	Weak transcription	Left Ventricle	heart
6	chr11:77533400-77553800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr11:77533400-77554000	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr11:77533400-77565600	Weak transcription	Gastric	stomach
9	chr11:77533400-77565600	Weak transcription	Pancreas	Pancrea
10	chr11:77533600-77552200	Weak transcription	Duodenum Smooth Muscle	Duodenum
11	chr11:77533600-77553000	Weak transcription	HUVEC	blood vessel
12	chr11:77534600-77555400	Weak transcription	Lung	lung
13	chr11:77535200-77551800	Weak transcription	Ovary	ovary
14	chr11:77535200-77552800	Weak transcription	Aorta	Aorta
15	chr11:77535200-77553800	Weak transcription	NHDF-Ad	bronchial
16	chr11:77535200-77554200	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr11:77535200-77554400	Weak transcription	HSMM	muscle
18	chr11:77535400-77552000	Weak transcription	Fetal Intestine Large	intestine
19	chr11:77535400-77552200	Weak transcription	Liver	Liver
20	chr11:77535400-77553400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr11:77535400-77553400	Weak transcription	Muscle Satellite Cultured Cells	--
22	chr11:77535400-77554200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr11:77535400-77555000	Weak transcription	Rectal Smooth Muscle	rectum
24	chr11:77535400-77565600	Weak transcription	HepG2	liver
25	chr11:77535800-77552000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr11:77535800-77552200	Weak transcription	Adipose Nuclei	Adipose
27	chr11:77535800-77552200	Weak transcription	Stomach Smooth Muscle	stomach
28	chr11:77536600-77552200	Weak transcription	Skeletal Muscle Female	skeletal muscle
29	chr11:77541600-77553800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
30	chr11:77543000-77552200	Weak transcription	Brain Cingulate Gyrus	brain
31	chr11:77544600-77552200	Weak transcription	Skeletal Muscle Male	skeletal muscle
32	chr11:77544600-77552400	Weak transcription	Psoas Muscle	Psoas
33	chr11:77544600-77552600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr11:77544600-77555400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
35	chr11:77544600-77564400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr11:77544600-77565400	Weak transcription	Spleen	Spleen
37	chr11:77544800-77551800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr11:77544800-77552400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
39	chr11:77544800-77553400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr11:77544800-77554200	Weak transcription	Duodenum Mucosa	Duodenum
41	chr11:77544800-77554200	Weak transcription	Dnd41	blood
42	chr11:77544800-77554400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr11:77544800-77564400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
44	chr11:77544800-77565400	Weak transcription	Pancreatic Islets	Pancreatic Islet
45	chr11:77545000-77554000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr11:77545000-77555400	Weak transcription	Fetal Kidney	kidney
47	chr11:77547200-77565800	Weak transcription	Fetal Heart	heart
48	chr11:77547600-77555200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
49	chr11:77548800-77582800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
50	chr11:77549000-77553400	Weak transcription	NH-A	brain

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