Variant report

Variant	rs12289316
Chromosome Location	chr11:77689297-77689298
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:77684778..77687771-chr11:77687903..77690145,2	K562	blood:

Extended variants
information (count: 48 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs11237326	0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11237328	0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11237329	0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11237333	0.86[EUR][1000 genomes]
rs11237335	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11237338	0.93[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11237341	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11237347	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11501934	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11603727	0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11605955	0.86[EUR][1000 genomes]
rs11606909	0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11606971	0.92[EUR][1000 genomes]
rs11607479	0.87[EUR][1000 genomes]
rs11607512	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12273552	0.88[EUR][1000 genomes]
rs12279880	0.93[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12284929	0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12292039	0.94[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12293597	0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12799701	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13377546	0.83[CEU][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17752458	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17825404	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1823507	0.94[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2305317	0.93[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4123593	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4123595	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs55878159	0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs55962013	0.82[EUR][1000 genomes]
rs57055061	0.83[EUR][1000 genomes]
rs7115801	0.93[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7119720	0.87[EUR][1000 genomes]
rs7131359	0.93[CEU][hapmap];0.89[CHB][hapmap];0.91[JPT][hapmap];0.87[EUR][1000 genomes]
rs72939500	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72941332	0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs72941339	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72941353	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9630225	0.88[CHB][hapmap];0.92[JPT][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[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	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
9	nsv526268	chr11:77688774-77698524	Strong transcription Weak transcription Enhancers Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12289316	INTS4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:77583400-77690000	Weak transcription	Colonic Mucosa	Colon
2	chr11:77592800-77690000	Weak transcription	Small Intestine	intestine
3	chr11:77597800-77690000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr11:77597800-77690000	Weak transcription	Esophagus	oesophagus
5	chr11:77597800-77690000	Weak transcription	Gastric	stomach
6	chr11:77602800-77690000	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr11:77614800-77700200	Weak transcription	Psoas Muscle	Psoas
8	chr11:77625800-77697400	Weak transcription	Rectal Smooth Muscle	rectum
9	chr11:77626000-77690000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr11:77626200-77689400	Weak transcription	Colon Smooth Muscle	Colon
11	chr11:77626600-77689600	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr11:77626600-77690000	Weak transcription	Pancreas	Pancrea
13	chr11:77645000-77690000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr11:77646200-77689600	Weak transcription	H1 Cell Line	embryonic stem cell
15	chr11:77648600-77690000	Weak transcription	Brain Germinal Matrix	brain
16	chr11:77649200-77701200	Weak transcription	NH-A	brain
17	chr11:77661400-77704400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr11:77664200-77689400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr11:77664200-77704000	Weak transcription	NHEK	skin
20	chr11:77665800-77689400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr11:77665800-77704200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr11:77666000-77704400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
23	chr11:77667600-77704200	Weak transcription	NHLF	lung
24	chr11:77668400-77689600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr11:77668400-77701200	Weak transcription	Aorta	Aorta
26	chr11:77668600-77690000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr11:77668600-77690000	Weak transcription	Lung	lung
28	chr11:77670000-77690000	Weak transcription	Spleen	Spleen
29	chr11:77670200-77689800	Weak transcription	HMEC	breast
30	chr11:77671000-77689800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr11:77671200-77704200	Weak transcription	NHDF-Ad	bronchial
32	chr11:77671800-77689600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
33	chr11:77671800-77689800	Weak transcription	Brain Angular Gyrus	brain
34	chr11:77672000-77689400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
35	chr11:77672000-77689600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
36	chr11:77672000-77689600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
37	chr11:77672000-77689800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
38	chr11:77672000-77689800	Weak transcription	HepG2	liver
39	chr11:77672000-77690400	Weak transcription	Hela-S3	cervix
40	chr11:77672000-77701200	Weak transcription	Brain Cingulate Gyrus	brain
41	chr11:77672000-77703800	Weak transcription	Fetal Brain Male	brain
42	chr11:77672200-77689400	Weak transcription	HUES48 Cell Line	embryonic stem cell
43	chr11:77672200-77689400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
44	chr11:77672200-77689400	Weak transcription	Brain Inferior Temporal Lobe	brain
45	chr11:77672200-77689600	Weak transcription	Brain Anterior Caudate	brain
46	chr11:77672200-77689800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
47	chr11:77672200-77689800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
48	chr11:77672200-77690000	Weak transcription	Ovary	ovary
49	chr11:77672200-77690000	Weak transcription	Sigmoid Colon	Sigmoid Colon
50	chr11:77673600-77689600	Weak transcription	Fetal Thymus	thymus

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