Variant report

Variant	rs12279880
Chromosome Location	chr11:77666487-77666488
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 57 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs11237326	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11237328	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11237329	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11237333	0.92[AFR][1000 genomes];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11237335	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11237338	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11237341	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11237347	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11501934	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11603727	0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11605955	0.88[EUR][1000 genomes]
rs11606909	0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11606971	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11607479	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11607512	0.93[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12273552	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12284929	0.90[AFR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12289316	0.93[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12289587	0.87[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs12292039	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12293597	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12799701	0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13377546	0.87[CEU][hapmap];0.91[YRI][hapmap];0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17752458	0.93[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17825404	0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1823507	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2305317	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4123593	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4123595	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs537811	0.83[GIH][hapmap]
rs55878159	0.98[AFR][1000 genomes];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs55962013	0.84[EUR][1000 genomes]
rs57055061	0.85[EUR][1000 genomes]
rs588217	0.83[GIH][hapmap]
rs648601	0.83[GIH][hapmap]
rs650171	0.83[GIH][hapmap]
rs663674	0.86[GIH][hapmap];0.84[MEX][hapmap]
rs695046	0.88[ASW][hapmap];0.86[GIH][hapmap];0.92[MEX][hapmap];1.00[YRI][hapmap]
rs7115801	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7119720	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7131359	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.87[YRI][hapmap];0.89[EUR][1000 genomes]
rs72939500	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72941332	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs72941339	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72941353	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7951033	0.83[GIH][hapmap]
rs947841	0.88[ASW][hapmap];0.86[GIH][hapmap];0.92[MEX][hapmap];1.00[YRI][hapmap]
rs9630225	0.85[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.82[YRI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12279880	INTS4	cis	cerebellum	SCAN
rs12279880	MRPL48	cis	parietal	SCAN
rs12279880	ALG8	cis	cerebellum	SCAN
rs12279880	THRSP	cis	cerebellum	SCAN

Chromatin state (count:115 , 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	chr11:77592800-77690000	Weak transcription	Small Intestine	intestine
4	chr11:77595800-77671000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
5	chr11:77597800-77669800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
6	chr11:77597800-77671000	Weak transcription	Fetal Brain Male	brain
7	chr11:77597800-77678200	Weak transcription	Skeletal Muscle Male	skeletal muscle
8	chr11:77597800-77690000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr11:77597800-77690000	Weak transcription	Esophagus	oesophagus
10	chr11:77597800-77690000	Weak transcription	Gastric	stomach
11	chr11:77602800-77690000	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr11:77614800-77700200	Weak transcription	Psoas Muscle	Psoas
13	chr11:77618200-77668200	Weak transcription	HUES48 Cell Line	embryonic stem cell
14	chr11:77619000-77667000	Weak transcription	Fetal Kidney	kidney
15	chr11:77619000-77668000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr11:77625800-77697400	Weak transcription	Rectal Smooth Muscle	rectum
17	chr11:77626000-77690000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr11:77626200-77689400	Weak transcription	Colon Smooth Muscle	Colon
19	chr11:77626600-77689600	Weak transcription	Rectal Mucosa Donor 31	rectum
20	chr11:77626600-77690000	Weak transcription	Pancreas	Pancrea
21	chr11:77627800-77684800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
22	chr11:77628000-77671000	Weak transcription	HSMM	muscle
23	chr11:77628400-77668000	Weak transcription	Skeletal Muscle Female	skeletal muscle
24	chr11:77629400-77668000	Weak transcription	Aorta	Aorta
25	chr11:77630200-77669600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
26	chr11:77639400-77667000	Weak transcription	Fetal Lung	lung
27	chr11:77639400-77670200	Weak transcription	Brain Cingulate Gyrus	brain
28	chr11:77639800-77668000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr11:77640000-77667800	Weak transcription	Duodenum Smooth Muscle	Duodenum
30	chr11:77641200-77669600	Weak transcription	K562	blood
31	chr11:77641600-77671000	Weak transcription	Hela-S3	cervix
32	chr11:77642200-77668000	Weak transcription	Rectal Mucosa Donor 29	rectum
33	chr11:77644600-77667200	Weak transcription	Primary T helper cells PMA-I stimulated	--
34	chr11:77644800-77667400	Weak transcription	Spleen	Spleen
35	chr11:77645000-77667200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr11:77645000-77680400	Weak transcription	Cortex derived primary cultured neurospheres	brain
37	chr11:77645000-77690000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr11:77646200-77689600	Weak transcription	H1 Cell Line	embryonic stem cell
39	chr11:77646400-77667000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
40	chr11:77648000-77670600	Weak transcription	GM12878-XiMat	blood
41	chr11:77648600-77690000	Weak transcription	Brain Germinal Matrix	brain
42	chr11:77648800-77667800	Weak transcription	Sigmoid Colon	Sigmoid Colon
43	chr11:77649000-77668000	Weak transcription	Primary T cells from cord blood	blood
44	chr11:77649200-77701200	Weak transcription	NH-A	brain
45	chr11:77654400-77670600	Weak transcription	Brain Hippocampus Middle	brain
46	chr11:77655000-77670600	Weak transcription	NHDF-Ad	bronchial
47	chr11:77655400-77684400	Weak transcription	Muscle Satellite Cultured Cells	--
48	chr11:77655800-77668000	Weak transcription	HepG2	liver
49	chr11:77655800-77669600	Weak transcription	Osteobl	bone
50	chr11:77656800-77666800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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