Variant report

Variant	rs12285765
Chromosome Location	chr11:77569035-77569036
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 54 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10899399	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10899404	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11237263	0.91[ASN][1000 genomes]
rs11237280	0.94[EUR][1000 genomes]
rs11237318	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11600140	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11606549	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11607032	0.81[ASN][1000 genomes]
rs12286317	0.91[ASN][1000 genomes]
rs17752006	0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs1783544	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2154972	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs24356	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2508189	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34130561	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4322421	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4344516	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs484363	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4945220	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs537811	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56218634	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs588217	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs598071	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs614495	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs621456	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs623173	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs623907	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs635195	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs636971	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs643388	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs648601	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs648896	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs650171	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs663674	0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs667225	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs668701	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs670090	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs684813	0.86[EUR][1000 genomes]
rs687037	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs694845	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs695046	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7122968	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7123080	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72945592	0.91[ASN][1000 genomes]
rs72947668	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs72949616	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs72949618	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7951033	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs947841	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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
5	nsv520740	chr11:77553638-77997936	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12285765	INTS4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:77548800-77582800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr11:77565400-77569200	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr11:77566000-77592600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
4	chr11:77566200-77569200	Strong transcription	Left Ventricle	heart
5	chr11:77566200-77569400	Strong transcription	Ovary	ovary
6	chr11:77566200-77571200	Weak transcription	Right Ventricle	heart
7	chr11:77566200-77577000	Weak transcription	Osteobl	bone
8	chr11:77566200-77579800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr11:77566200-77580000	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr11:77566200-77580400	Weak transcription	Primary T helper cells fromperipheralblood	blood
11	chr11:77566200-77580600	Weak transcription	HSMM	muscle
12	chr11:77566200-77582000	Weak transcription	Muscle Satellite Cultured Cells	--
13	chr11:77566200-77582600	Weak transcription	Colonic Mucosa	Colon
14	chr11:77566200-77583200	Weak transcription	Pancreas	Pancrea
15	chr11:77566200-77589000	Weak transcription	NHLF	lung
16	chr11:77566200-77589600	Weak transcription	Esophagus	oesophagus
17	chr11:77566200-77594600	Weak transcription	Colon Smooth Muscle	Colon
18	chr11:77566400-77576200	Weak transcription	NHDF-Ad	bronchial
19	chr11:77566400-77576600	Weak transcription	NH-A	brain
20	chr11:77566400-77582000	Weak transcription	Primary T helper cells PMA-I stimulated	--
21	chr11:77566400-77582800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr11:77566400-77583000	Weak transcription	Spleen	Spleen
23	chr11:77566600-77569400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
24	chr11:77566600-77569800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr11:77566600-77580200	Weak transcription	Monocytes-CD14+_RO01746	blood
26	chr11:77566800-77574800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
27	chr11:77566800-77580200	Weak transcription	Sigmoid Colon	Sigmoid Colon
28	chr11:77566800-77587800	Weak transcription	A549	lung
29	chr11:77567000-77569800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr11:77567000-77569800	Strong transcription	Lung	lung
31	chr11:77567000-77570000	Strong transcription	Fetal Stomach	stomach
32	chr11:77567000-77580600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
33	chr11:77567000-77581800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
34	chr11:77567000-77582600	Weak transcription	HUVEC	blood vessel
35	chr11:77567000-77586600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
36	chr11:77567400-77573000	Weak transcription	Stomach Smooth Muscle	stomach
37	chr11:77567400-77582600	Weak transcription	Placenta	Placenta
38	chr11:77567600-77577000	Weak transcription	HSMMtube	muscle
39	chr11:77567600-77582600	Weak transcription	Primary T cells from cord blood	blood
40	chr11:77567600-77589600	Weak transcription	HepG2	liver
41	chr11:77567800-77571200	Weak transcription	Fetal Heart	heart
42	chr11:77567800-77574000	Weak transcription	Gastric	stomach
43	chr11:77567800-77579600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr11:77567800-77580600	Weak transcription	Rectal Smooth Muscle	rectum
45	chr11:77567800-77582400	Weak transcription	Brain Inferior Temporal Lobe	brain
46	chr11:77567800-77582600	Weak transcription	Primary B cells from cord blood	blood
47	chr11:77567800-77582800	Weak transcription	Brain Substantia Nigra	brain
48	chr11:77567800-77582800	Weak transcription	Fetal Brain Female	brain
49	chr11:77567800-77589400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
50	chr11:77567800-77594800	Weak transcription	Brain Angular Gyrus	brain

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