Variant report

Variant	rs558470
Chromosome Location	chr11:77106700-77106701
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOS	chr11:77106606-77106820	MCF10A-Er-Src	breast:	n/a	n/a
2	FOS	chr11:77106560-77106833	MCF10A-Er-Src	breast:	n/a	n/a
3	STAT3	chr11:77106493-77106830	MCF10A-Er-Src	breast:	n/a	n/a
4	STAT3	chr11:77106560-77106760	MCF10A-Er-Src	breast:	n/a	n/a
5	RCOR1	chr11:77106608-77106745	GM12878	blood:	n/a	n/a

Variant related genes	Relation type
PAK1	TF binding region

Extended variants
information (count: 111 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:103)

rs_ID	r²[population]
rs11237123	1.00[JPT][hapmap]
rs11237141	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs11237142	0.96[ASN][1000 genomes]
rs11237148	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs11237150	1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs11237151	0.96[ASN][1000 genomes]
rs11237164	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs1125619	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs11512967	0.86[ASN][1000 genomes]
rs1225478	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12361757	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs12363707	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs12363842	0.96[ASN][1000 genomes]
rs12363944	1.00[CHB][hapmap];0.89[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap]
rs12366261	0.81[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.92[ASN][1000 genomes]
rs1237490	0.88[EUR][1000 genomes]
rs12794253	0.96[ASN][1000 genomes]
rs1377472	0.96[ASN][1000 genomes]
rs1597954	0.88[ASN][1000 genomes]
rs1622364	0.96[ASN][1000 genomes]
rs1670446	0.96[ASN][1000 genomes]
rs1670449	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs1670450	0.96[ASN][1000 genomes]
rs1670456	0.96[ASN][1000 genomes]
rs1670458	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs1670461	0.92[ASN][1000 genomes]
rs1670462	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.88[TSI][hapmap];0.92[ASN][1000 genomes]
rs17824184	0.81[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.96[ASN][1000 genomes]
rs1793468	0.96[ASN][1000 genomes]
rs1793471	0.92[ASN][1000 genomes]
rs1793472	0.96[ASN][1000 genomes]
rs1793487	0.96[ASN][1000 genomes]
rs1793490	0.92[ASN][1000 genomes]
rs2154754	0.96[CEU][hapmap];0.83[EUR][1000 genomes]
rs2156567	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2602476	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2602483	0.96[ASN][1000 genomes]
rs2602487	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2725820	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2725822	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2725825	0.96[ASN][1000 genomes]
rs2725828	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3015982	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3015983	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3015985	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];0.97[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3015986	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3015988	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.97[TSI][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3015990	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3015992	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3019233	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3019234	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3019235	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3019236	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3019249	0.87[EUR][1000 genomes]
rs3019257	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34025917	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34880271	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4375461	0.96[ASN][1000 genomes]
rs472691	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[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];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs476258	0.88[EUR][1000 genomes]
rs479104	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs493256	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs494289	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs503406	0.96[EUR][1000 genomes]
rs505841	0.88[EUR][1000 genomes]
rs508662	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs51500	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs520938	0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs522015	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs523481	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs531638	0.87[EUR][1000 genomes]
rs535008	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs552323	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs557484	0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs560571	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs561386	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];0.97[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs562845	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs563731	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs572485	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs576220	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs580624	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs592602	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs595654	0.87[EUR][1000 genomes]
rs598801	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs644551	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs649040	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs653792	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs657269	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs66518011	0.92[ASN][1000 genomes]
rs66540426	0.96[ASN][1000 genomes]
rs66728428	0.96[ASN][1000 genomes]
rs674259	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs683455	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs683762	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs684793	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs686068	1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs689108	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7110378	1.00[YRI][hapmap]
rs7118943	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7934230	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7949721	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs883224	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs883680	0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1048360	chr11:76900813-77387933	Strong transcription Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
2	nsv541089	chr11:76900813-77387933	Active TSS Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	nsv1049603	chr11:76900813-77520411	Strong transcription Weak transcription Active TSS Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
4	nsv541090	chr11:76900813-77520411	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
5	esv3424135	chr11:76961603-77277087	Strong transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Enhancers Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
6	nsv1037724	chr11:77061945-77250391	Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	nsv541091	chr11:77061945-77250391	Weak transcription Active TSS Enhancers Strong transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
8	esv3437433	chr11:77101280-77291686	Flanking Bivalent TSS/Enh Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs558470	PAK1	cis	parietal	SCAN
rs558470	KCTD14	cis	cerebellum	SCAN
rs558470	RSF1	cis	cerebellum	SCAN
rs558470	KCTD14	cis	parietal	SCAN

Chromatin state (count:78 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:77046800-77121600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr11:77055200-77117600	Weak transcription	Pancreas	Pancrea
3	chr11:77067200-77111800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr11:77084000-77111400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr11:77084200-77107000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr11:77084600-77121200	Weak transcription	Thymus	Thymus
7	chr11:77086400-77108000	Weak transcription	Brain Anterior Caudate	brain
8	chr11:77086600-77120000	Weak transcription	Spleen	Spleen
9	chr11:77087200-77106800	Weak transcription	NHEK	skin
10	chr11:77090800-77111200	Weak transcription	HMEC	breast
11	chr11:77091000-77106800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr11:77091000-77108200	Weak transcription	Brain Angular Gyrus	brain
13	chr11:77091000-77112000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr11:77091000-77113400	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr11:77091000-77117000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
16	chr11:77091000-77117600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr11:77091800-77106800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
18	chr11:77092000-77106800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr11:77093600-77117800	Weak transcription	NH-A	brain
20	chr11:77094000-77118400	Weak transcription	NHLF	lung
21	chr11:77094200-77111800	Weak transcription	Muscle Satellite Cultured Cells	--
22	chr11:77094200-77118200	Weak transcription	NHDF-Ad	bronchial
23	chr11:77094200-77118400	Weak transcription	Colonic Mucosa	Colon
24	chr11:77095400-77106800	Weak transcription	H1 Cell Line	embryonic stem cell
25	chr11:77095400-77121000	Weak transcription	Fetal Thymus	thymus
26	chr11:77095800-77118600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr11:77097800-77111200	Weak transcription	Brain Cingulate Gyrus	brain
28	chr11:77097800-77111200	Weak transcription	Fetal Muscle Leg	muscle
29	chr11:77098000-77121200	Weak transcription	Placenta	Placenta
30	chr11:77098200-77118400	Weak transcription	Fetal Stomach	stomach
31	chr11:77102600-77112400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
32	chr11:77102800-77106800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
33	chr11:77102800-77106800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr11:77102800-77111800	Weak transcription	Fetal Lung	lung
35	chr11:77102800-77116400	Weak transcription	Primary T helper cells PMA-I stimulated	--
36	chr11:77103000-77107000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
37	chr11:77103000-77118400	Weak transcription	Primary hematopoietic stem cells	blood
38	chr11:77103000-77121400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
39	chr11:77103200-77106800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr11:77103200-77108600	Weak transcription	HUES6 Cell Line	embryonic stem cell
41	chr11:77103200-77112800	Weak transcription	Primary B cells from cord blood	blood
42	chr11:77103600-77107000	Weak transcription	Primary monocytes fromperipheralblood	blood
43	chr11:77103600-77109600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr11:77103800-77106800	Weak transcription	HUES64 Cell Line	embryonic stem cell
45	chr11:77103800-77121000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
46	chr11:77103800-77122000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr11:77104000-77106800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr11:77104000-77108000	Weak transcription	Rectal Smooth Muscle	rectum
49	chr11:77104000-77112600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr11:77104200-77107600	Weak transcription	Monocytes-CD14+_RO01746	blood

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