Variant report

Variant	rs12293597
Chromosome Location	chr11:77645505-77645506
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 50 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs11237326	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11237328	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11237329	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11237333	0.85[EUR][1000 genomes]
rs11237335	0.83[AFR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11237338	0.83[AFR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11237341	0.81[AFR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11237347	0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11501934	0.83[AFR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11603727	0.89[EUR][1000 genomes]
rs11605955	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11606909	0.89[EUR][1000 genomes]
rs11606971	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11607043	0.80[ASN][1000 genomes]
rs11607479	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11607512	0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12273552	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12279880	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12284929	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12289316	0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12289587	0.84[AMR][1000 genomes]
rs12292039	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12799701	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13377546	0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17752458	0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17825404	0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1823507	0.87[AFR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2305317	0.93[AFR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4123593	0.86[AFR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4123595	0.87[AFR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs55878159	0.86[AFR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs55962013	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs57055061	0.89[EUR][1000 genomes]
rs7115801	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7119720	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7131359	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72939500	0.93[AFR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72941332	0.89[EUR][1000 genomes]
rs72941339	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs72941353	0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9630225	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 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
6	nsv1035753	chr11:77577384-77866386	Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
7	nsv541093	chr11:77577384-77866386	Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
8	nsv975205	chr11:77628075-77671380	Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
9	nsv8841	chr11:77641044-77692578	Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12293597	INTS4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:77583400-77670600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr11:77583400-77690000	Weak transcription	Colonic Mucosa	Colon
3	chr11:77591800-77650400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr11:77592800-77690000	Weak transcription	Small Intestine	intestine
5	chr11:77595800-77671000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
6	chr11:77597800-77669800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
7	chr11:77597800-77671000	Weak transcription	Fetal Brain Male	brain
8	chr11:77597800-77678200	Weak transcription	Skeletal Muscle Male	skeletal muscle
9	chr11:77597800-77690000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr11:77597800-77690000	Weak transcription	Esophagus	oesophagus
11	chr11:77597800-77690000	Weak transcription	Gastric	stomach
12	chr11:77602800-77690000	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr11:77603200-77650200	Weak transcription	Fetal Brain Female	brain
14	chr11:77614800-77700200	Weak transcription	Psoas Muscle	Psoas
15	chr11:77615000-77656400	Weak transcription	Right Ventricle	heart
16	chr11:77618200-77668200	Weak transcription	HUES48 Cell Line	embryonic stem cell
17	chr11:77619000-77667000	Weak transcription	Fetal Kidney	kidney
18	chr11:77619000-77668000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr11:77625800-77665600	Weak transcription	HSMMtube	muscle
20	chr11:77625800-77697400	Weak transcription	Rectal Smooth Muscle	rectum
21	chr11:77626000-77666200	Weak transcription	Brain Substantia Nigra	brain
22	chr11:77626000-77690000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr11:77626200-77665400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr11:77626200-77689400	Weak transcription	Colon Smooth Muscle	Colon
25	chr11:77626600-77665600	Weak transcription	Ovary	ovary
26	chr11:77626600-77689600	Weak transcription	Rectal Mucosa Donor 31	rectum
27	chr11:77626600-77690000	Weak transcription	Pancreas	Pancrea
28	chr11:77627800-77684800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
29	chr11:77628000-77646000	Weak transcription	Primary T cells from cord blood	blood
30	chr11:77628000-77671000	Weak transcription	HSMM	muscle
31	chr11:77628400-77668000	Weak transcription	Skeletal Muscle Female	skeletal muscle
32	chr11:77629400-77653400	Weak transcription	Brain Inferior Temporal Lobe	brain
33	chr11:77629400-77668000	Weak transcription	Aorta	Aorta
34	chr11:77630000-77648000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr11:77630000-77665400	Weak transcription	Lung	lung
36	chr11:77630200-77669600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
37	chr11:77630600-77665400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr11:77638000-77646000	Weak transcription	Brain Germinal Matrix	brain
39	chr11:77638000-77647600	Weak transcription	Fetal Muscle Trunk	muscle
40	chr11:77638000-77653200	Weak transcription	Muscle Satellite Cultured Cells	--
41	chr11:77638200-77646000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
42	chr11:77638200-77647400	Weak transcription	Sigmoid Colon	Sigmoid Colon
43	chr11:77638200-77657200	Weak transcription	Primary B cells from cord blood	blood
44	chr11:77638200-77665400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
45	chr11:77638200-77665600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
46	chr11:77638600-77665400	Weak transcription	Placenta	Placenta
47	chr11:77639000-77649200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
48	chr11:77639200-77647800	Weak transcription	Primary B cells from peripheral blood	blood
49	chr11:77639400-77647800	Weak transcription	GM12878-XiMat	blood
50	chr11:77639400-77665400	Weak transcription	Stomach Smooth Muscle	stomach

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