Variant report

Variant	rs11022
Chromosome Location	chr15:42824578-42824579
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:42802411..42804799-chr15:42823658..42825674,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-LRRC57-1	chr15:42824528-42825038	ENSG00000261684.1

Variant related genes	Relation type
ENSG00000092531	Chromatin interaction

Extended variants
information (count: 92 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:88)

rs_ID	r²[population]
rs10454039	0.90[EUR][1000 genomes]
rs10518763	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10518766	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1060291	0.88[ASW][hapmap];0.95[CEU][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1060293	1.00[ASN][1000 genomes]
rs10851410	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10851411	0.86[CEU][hapmap];0.84[TSI][hapmap];0.88[EUR][1000 genomes]
rs11070374	0.95[CEU][hapmap];0.89[EUR][1000 genomes]
rs11070376	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11631193	0.88[EUR][1000 genomes]
rs11636577	0.81[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11638208	0.86[EUR][1000 genomes]
rs12324113	0.93[EUR][1000 genomes]
rs12324717	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12903432	0.95[EUR][1000 genomes]
rs12906697	0.90[EUR][1000 genomes]
rs12913324	0.82[EUR][1000 genomes]
rs16973089	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs16973091	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs16973093	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs16973095	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs16973096	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs16973097	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs16973107	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs16973109	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs16973132	1.00[CHB][hapmap]
rs16973137	1.00[CHB][hapmap]
rs16973148	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs16973153	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs16973155	1.00[CHB][hapmap]
rs16973171	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs16973174	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs16973175	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs16973320	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs17709180	1.00[ASN][1000 genomes]
rs17709377	1.00[ASN][1000 genomes]
rs17766532	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1900921	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2241998	1.00[CEU][hapmap];0.84[TSI][hapmap];0.88[EUR][1000 genomes]
rs2255995	0.95[EUR][1000 genomes]
rs2412704	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2595939	0.95[EUR][1000 genomes]
rs2595940	0.95[CEU][hapmap];0.87[TSI][hapmap];0.95[EUR][1000 genomes]
rs2595941	0.94[EUR][1000 genomes]
rs2617236	0.95[CEU][hapmap];0.87[TSI][hapmap];0.92[EUR][1000 genomes]
rs28364347	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs28886308	0.84[EUR][1000 genomes]
rs2899051	0.90[CEU][hapmap];1.00[CHB][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2899057	0.89[EUR][1000 genomes]
rs2899059	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs34359922	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs34643746	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34792942	1.00[ASN][1000 genomes]
rs3986280	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4344713	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4573906	0.95[EUR][1000 genomes]
rs4923948	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4924684	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4924687	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs56357092	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56982416	1.00[ASN][1000 genomes]
rs58042601	1.00[ASN][1000 genomes]
rs58641431	1.00[ASN][1000 genomes]
rs59697584	1.00[ASN][1000 genomes]
rs59705032	1.00[ASN][1000 genomes]
rs60380503	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60584955	1.00[ASN][1000 genomes]
rs60812675	1.00[ASN][1000 genomes]
rs61489160	1.00[ASN][1000 genomes]
rs62022317	1.00[ASN][1000 genomes]
rs7164437	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7164874	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7165023	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7178901	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7180483	1.00[ASN][1000 genomes]
rs7182797	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs73402783	1.00[ASN][1000 genomes]
rs73402785	1.00[ASN][1000 genomes]
rs73404714	1.00[ASN][1000 genomes]
rs73404723	1.00[ASN][1000 genomes]
rs73404730	1.00[ASN][1000 genomes]
rs73404763	1.00[ASN][1000 genomes]
rs73406518	1.00[ASN][1000 genomes]
rs73406534	1.00[ASN][1000 genomes]
rs73406545	1.00[ASN][1000 genomes]
rs74009095	1.00[ASN][1000 genomes]
rs8033412	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9302112	0.95[CEU][hapmap];0.87[TSI][hapmap];0.95[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1049445	chr15:42239738-42830484	Enhancers Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
2	nsv542366	chr15:42239738-42830484	Weak transcription Active TSS Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
3	esv3334708	chr15:42664344-42827738	Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
4	nsv528725	chr15:42755555-43104406	Weak transcription Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11022	CEP27	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:42793000-42835600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr15:42793800-42837200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
3	chr15:42797400-42839800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr15:42797600-42839400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr15:42799200-42839400	Weak transcription	Stomach Mucosa	stomach
6	chr15:42802400-42839200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr15:42803200-42837200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr15:42803600-42839400	Weak transcription	A549	lung
9	chr15:42804000-42826800	Strong transcription	HUVEC	blood vessel
10	chr15:42804600-42836400	Strong transcription	Primary neutrophils fromperipheralblood	blood
11	chr15:42804800-42825400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr15:42804800-42828800	Strong transcription	Placenta	Placenta
13	chr15:42804800-42836400	Strong transcription	Primary monocytes fromperipheralblood	blood
14	chr15:42804800-42836400	Strong transcription	Monocytes-CD14+_RO01746	blood
15	chr15:42805200-42825800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr15:42805400-42836800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr15:42806200-42836400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr15:42806200-42839000	Weak transcription	Fetal Brain Male	brain
19	chr15:42808200-42824800	Weak transcription	Hela-S3	cervix
20	chr15:42808400-42839000	Weak transcription	Fetal Heart	heart
21	chr15:42808800-42836000	Weak transcription	Esophagus	oesophagus
22	chr15:42810200-42831000	Weak transcription	Gastric	stomach
23	chr15:42810200-42840200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr15:42811000-42837600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
25	chr15:42811200-42828600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
26	chr15:42811200-42831200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
27	chr15:42811800-42836000	Weak transcription	Colonic Mucosa	Colon
28	chr15:42812000-42828400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr15:42815400-42826000	Strong transcription	HSMM	muscle
30	chr15:42815800-42825200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr15:42815800-42833000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
32	chr15:42816400-42827000	Strong transcription	Liver	Liver
33	chr15:42817400-42840200	Weak transcription	Pancreas	Pancrea
34	chr15:42818800-42826000	Weak transcription	Pancreatic Islets	Pancreatic Islet
35	chr15:42819600-42824600	Strong transcription	Fetal Muscle Trunk	muscle
36	chr15:42819600-42828200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr15:42819800-42824600	Strong transcription	Sigmoid Colon	Sigmoid Colon
38	chr15:42819800-42824800	Strong transcription	Fetal Intestine Large	intestine
39	chr15:42819800-42825000	Strong transcription	Stomach Smooth Muscle	stomach
40	chr15:42819800-42825800	Strong transcription	HUES64 Cell Line	embryonic stem cell
41	chr15:42819800-42826200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
42	chr15:42819800-42828800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
43	chr15:42820000-42824600	Strong transcription	Osteobl	bone
44	chr15:42820000-42825600	Strong transcription	Primary B cells from peripheral blood	blood
45	chr15:42820000-42825800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
46	chr15:42820000-42827600	Strong transcription	Skeletal Muscle Female	skeletal muscle
47	chr15:42820000-42828400	Strong transcription	Primary B cells from cord blood	blood
48	chr15:42820000-42828800	Strong transcription	Duodenum Mucosa	Duodenum
49	chr15:42820000-42829000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr15:42820000-42831400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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