Variant report

Variant	rs17752458
Chromosome Location	chr11:77702484-77702485
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:77699025..77702631-chr11:77704128..77707034,4	K562	blood:
2	chr11:77701991..77703904-chr11:77704276..77705898,2	MCF-7	breast:
3	chr11:77530485..77532728-chr11:77700651..77703314,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000048649	Chromatin interaction
ENSG00000087884	Chromatin interaction
ENSG00000149262	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs11237326	0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11237328	0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11237329	0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11237333	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11237335	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11237338	0.93[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11237341	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11237347	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11501934	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11603727	0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11605955	0.86[EUR][1000 genomes]
rs11606909	0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11606971	0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11607479	0.87[EUR][1000 genomes]
rs11607512	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12273552	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12279880	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]
rs12284929	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12289316	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]
rs12289587	0.82[ASN][1000 genomes]
rs12292039	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12293597	0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12799701	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13377546	0.81[CEU][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17825404	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1823507	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2305317	0.93[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4123593	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4123595	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs55878159	0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs55962013	0.82[EUR][1000 genomes]
rs57055061	0.83[EUR][1000 genomes]
rs588217	0.83[GIH][hapmap];0.84[MEX][hapmap]
rs621456	0.83[MEX][hapmap]
rs623173	0.84[MEX][hapmap]
rs648601	0.83[GIH][hapmap];0.84[MEX][hapmap]
rs663674	0.86[GIH][hapmap];0.92[MEX][hapmap]
rs668701	0.84[MEX][hapmap]
rs695046	0.86[GIH][hapmap];1.00[MEX][hapmap]
rs7115801	0.93[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7119720	0.87[EUR][1000 genomes]
rs7131359	0.93[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.87[EUR][1000 genomes]
rs72939500	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72941332	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72941339	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72941353	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7951033	0.83[GIH][hapmap];0.84[MEX][hapmap]
rs947841	0.86[GIH][hapmap];1.00[MEX][hapmap]
rs9630225	1.00[CHB][hapmap];0.92[JPT][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs17752458	INTS4	cis	cerebellum	SCAN
rs17752458	INTS4	Cis_1M	lymphoblastoid	RTeQTL
rs17752458	MRPL48	cis	parietal	SCAN
rs17752458	ALG8	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:77661400-77704400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr11:77664200-77704000	Weak transcription	NHEK	skin
3	chr11:77665800-77704200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr11:77666000-77704400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr11:77667600-77704200	Weak transcription	NHLF	lung
6	chr11:77671200-77704200	Weak transcription	NHDF-Ad	bronchial
7	chr11:77672000-77703800	Weak transcription	Fetal Brain Male	brain
8	chr11:77679000-77704200	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr11:77681000-77704200	Weak transcription	HSMMtube	muscle
10	chr11:77688200-77704800	Weak transcription	Stomach Mucosa	stomach
11	chr11:77688600-77702800	Strong transcription	Primary T helper cells fromperipheralblood	blood
12	chr11:77688800-77703400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr11:77688800-77703400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
14	chr11:77688800-77703800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr11:77689000-77702600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
16	chr11:77689000-77704800	Weak transcription	Fetal Heart	heart
17	chr11:77689200-77703000	Strong transcription	Primary T cells from cord blood	blood
18	chr11:77689200-77704800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr11:77689600-77703000	Strong transcription	Fetal Thymus	thymus
20	chr11:77690400-77704200	Weak transcription	HMEC	breast
21	chr11:77690600-77703800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
22	chr11:77690600-77704000	Weak transcription	Brain Anterior Caudate	brain
23	chr11:77690600-77704000	Weak transcription	Brain Substantia Nigra	brain
24	chr11:77690600-77704200	Weak transcription	Gastric	stomach
25	chr11:77690600-77704200	Weak transcription	Skeletal Muscle Male	skeletal muscle
26	chr11:77690600-77704400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr11:77690800-77704200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr11:77690800-77704200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
29	chr11:77690800-77704200	Weak transcription	Small Intestine	intestine
30	chr11:77691400-77704000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
31	chr11:77691400-77704800	Weak transcription	Colonic Mucosa	Colon
32	chr11:77692000-77704000	Weak transcription	Colon Smooth Muscle	Colon
33	chr11:77692600-77704000	Weak transcription	A549	lung
34	chr11:77692600-77704200	Weak transcription	HUVEC	blood vessel
35	chr11:77695400-77702600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr11:77696000-77703000	Strong transcription	Primary T cells fromperipheralblood	blood
37	chr11:77696200-77703400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr11:77696400-77704400	Weak transcription	Fetal Kidney	kidney
39	chr11:77696600-77702600	Strong transcription	HUES64 Cell Line	embryonic stem cell
40	chr11:77696800-77703200	Strong transcription	Adipose Nuclei	Adipose
41	chr11:77696800-77703400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr11:77697000-77702600	Strong transcription	Fetal Muscle Leg	muscle
43	chr11:77697000-77703200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
44	chr11:77697200-77703000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr11:77697600-77703000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr11:77697800-77703400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr11:77698000-77702600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
48	chr11:77698000-77702600	Strong transcription	Cortex derived primary cultured neurospheres	brain
49	chr11:77698000-77703000	Strong transcription	Placenta	Placenta
50	chr11:77698200-77703000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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