Variant report

Variant	rs616018
Chromosome Location	chr11:86231119-86231120
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:86227984..86231236-chr11:86233662..86235563,3	MCF-7	breast:
2	chr11:86209488..86213127-chr11:86228780..86231761,3	K562	blood:
3	chr11:86213664..86215270-chr11:86230808..86233589,2	MCF-7	breast:
4	chr11:86224834..86227420-chr11:86229553..86231855,2	K562	blood:
5	chr11:86225920..86228246-chr11:86229553..86231799,2	K562	blood:

Extended variants
information (count: 98 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:94)

rs_ID	r²[population]
rs10431169	0.81[CHB][hapmap]
rs10501620	0.82[CHB][hapmap]
rs10501621	0.82[CHB][hapmap]
rs147045	0.95[CHB][hapmap]
rs1841066	1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2279046	0.95[CHB][hapmap];0.94[CHD][hapmap];0.84[GIH][hapmap];0.84[ASN][1000 genomes]
rs2446226	0.81[ASN][1000 genomes]
rs2446228	0.95[CHB][hapmap];0.97[CHD][hapmap];0.84[GIH][hapmap];0.90[ASN][1000 genomes]
rs2446229	0.83[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.97[TSI][hapmap];0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2446231	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2511090	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs36043971	0.85[ASN][1000 genomes]
rs3781812	0.82[CHB][hapmap];0.83[CHD][hapmap]
rs498981	0.89[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];0.89[MKK][hapmap];1.00[TSI][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs501362	0.98[ASN][1000 genomes]
rs502749	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs503583	0.95[CHB][hapmap];0.85[ASN][1000 genomes]
rs509870	0.84[ASN][1000 genomes]
rs511884	0.95[CHB][hapmap];0.83[ASN][1000 genomes]
rs525764	1.00[CHB][hapmap];0.87[ASN][1000 genomes]
rs531908	0.98[ASN][1000 genomes]
rs535652	0.95[CHB][hapmap];0.89[CHD][hapmap];0.83[ASN][1000 genomes]
rs553351	1.00[CHB][hapmap];0.86[CHD][hapmap];0.84[JPT][hapmap];0.91[ASN][1000 genomes]
rs582976	0.95[CHB][hapmap];0.83[ASN][1000 genomes]
rs585527	0.85[ASN][1000 genomes]
rs588287	0.95[CHB][hapmap];0.94[CHD][hapmap];0.84[ASN][1000 genomes]
rs589174	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs589368	0.95[CHB][hapmap];0.83[ASN][1000 genomes]
rs590401	0.91[CHB][hapmap]
rs593853	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs594106	0.82[ASN][1000 genomes]
rs596056	0.95[CHB][hapmap];0.87[ASN][1000 genomes]
rs597296	0.95[CHB][hapmap];0.85[ASN][1000 genomes]
rs597793	0.98[ASN][1000 genomes]
rs598187	0.85[ASN][1000 genomes]
rs601300	0.86[CHB][hapmap];0.85[CHD][hapmap]
rs601824	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs603890	0.85[ASN][1000 genomes]
rs605251	0.91[CHB][hapmap];0.85[CHD][hapmap]
rs605618	0.95[CHB][hapmap];0.91[CHD][hapmap];0.83[ASN][1000 genomes]
rs606546	0.81[ASN][1000 genomes]
rs608180	0.85[ASN][1000 genomes]
rs609848	0.94[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs610842	1.00[CHB][hapmap];0.97[CHD][hapmap];0.91[ASN][1000 genomes]
rs612163	0.95[CHB][hapmap];0.91[CHD][hapmap];0.85[ASN][1000 genomes]
rs613412	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs618513	0.91[CHB][hapmap];0.88[CHD][hapmap]
rs61904415	0.84[ASN][1000 genomes]
rs619195	0.95[CHB][hapmap];0.86[ASN][1000 genomes]
rs619472	0.89[ASN][1000 genomes]
rs623478	1.00[CHB][hapmap];0.97[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs624236	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs624843	1.00[CHB][hapmap];0.91[ASN][1000 genomes]
rs624870	0.90[CHB][hapmap];0.81[ASN][1000 genomes]
rs625925	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs628406	0.95[CHB][hapmap];0.84[ASN][1000 genomes]
rs628449	0.98[ASN][1000 genomes]
rs630438	0.90[ASN][1000 genomes]
rs632538	0.82[ASN][1000 genomes]
rs634509	0.95[CHB][hapmap];0.88[CHD][hapmap];0.81[ASN][1000 genomes]
rs635934	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs636485	0.90[CHB][hapmap];0.85[ASN][1000 genomes]
rs638041	0.95[CHB][hapmap];0.94[CHD][hapmap];0.85[ASN][1000 genomes]
rs640310	0.95[CHB][hapmap];0.85[ASN][1000 genomes]
rs642278	0.95[ASN][1000 genomes]
rs643950	0.84[ASN][1000 genomes]
rs644086	0.86[CHB][hapmap];0.94[CHD][hapmap];0.84[GIH][hapmap];0.90[ASN][1000 genomes]
rs646691	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs646798	0.85[ASN][1000 genomes]
rs648798	1.00[CHB][hapmap];0.86[CHD][hapmap];0.83[ASN][1000 genomes]
rs651089	0.91[CHB][hapmap];0.85[CHD][hapmap]
rs653779	0.95[CHB][hapmap];0.91[CHD][hapmap];0.85[ASN][1000 genomes]
rs655868	0.81[ASN][1000 genomes]
rs655934	0.89[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.94[MEX][hapmap];0.92[MKK][hapmap];0.97[TSI][hapmap];0.85[YRI][hapmap];0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs658166	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs659405	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.96[ASN][1000 genomes]
rs661083	0.85[ASN][1000 genomes]
rs661972	0.85[ASN][1000 genomes]
rs662361	0.95[CHB][hapmap];0.94[CHD][hapmap];0.84[GIH][hapmap];0.84[ASN][1000 genomes]
rs663262	0.90[CHB][hapmap]
rs668270	0.85[ASN][1000 genomes]
rs668272	0.89[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.81[MKK][hapmap];1.00[YRI][hapmap]
rs670602	0.90[ASN][1000 genomes]
rs674250	0.85[ASN][1000 genomes]
rs677700	0.90[CHB][hapmap]
rs679076	0.91[CHB][hapmap];0.91[CHD][hapmap]
rs679382	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs680846	0.83[ASN][1000 genomes]
rs681158	0.85[ASN][1000 genomes]
rs687804	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.95[JPT][hapmap];0.94[MEX][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs689039	0.84[ASN][1000 genomes]
rs694952	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7130920	1.00[CHB][hapmap];0.97[CHD][hapmap];0.84[GIH][hapmap];0.87[ASN][1000 genomes]
rs9645702	0.84[ASN][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	nsv1044081	chr11:86133641-86868560	Bivalent/Poised TSS Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv541118	chr11:86133641-86868560	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
3	nsv898056	chr11:86156848-86304402	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
4	nsv555665	chr11:86230898-86417553	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs616018	PCF11	cis	parietal	SCAN

Chromatin state (count:76 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:86223000-86238200	Weak transcription	Pancreas	Pancrea
2	chr11:86223800-86236800	Weak transcription	Primary hematopoietic stem cells	blood
3	chr11:86223800-86237000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr11:86224800-86232400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr11:86225400-86233200	Enhancers	HUVEC	blood vessel
6	chr11:86225800-86231400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr11:86226200-86231600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr11:86226400-86231400	Enhancers	Osteobl	bone
9	chr11:86227000-86234800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr11:86227000-86235000	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr11:86227000-86235600	Weak transcription	Rectal Mucosa Donor 29	rectum
12	chr11:86227800-86231800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr11:86228000-86232000	Enhancers	Hela-S3	cervix
14	chr11:86228600-86231200	Enhancers	ES-I3 Cell Line	embryonic stem cell
15	chr11:86229200-86231400	Enhancers	Fetal Muscle Leg	muscle
16	chr11:86229200-86231800	Enhancers	Cortex derived primary cultured neurospheres	brain
17	chr11:86229200-86232000	Enhancers	Fetal Lung	lung
18	chr11:86229400-86231400	Enhancers	Fetal Brain Female	brain
19	chr11:86229400-86231400	Enhancers	Fetal Stomach	stomach
20	chr11:86229400-86231800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr11:86229400-86231800	Enhancers	Fetal Brain Male	brain
22	chr11:86229400-86232200	Enhancers	Fetal Heart	heart
23	chr11:86229600-86231200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr11:86229600-86231200	Enhancers	Muscle Satellite Cultured Cells	--
25	chr11:86229600-86231200	Enhancers	Small Intestine	intestine
26	chr11:86229600-86231400	Enhancers	NH-A	brain
27	chr11:86229600-86231400	Enhancers	NHDF-Ad	bronchial
28	chr11:86229600-86231600	Enhancers	Brain Germinal Matrix	brain
29	chr11:86229600-86232200	Enhancers	Right Ventricle	heart
30	chr11:86229800-86231400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr11:86229800-86231400	Enhancers	Brain Angular Gyrus	brain
32	chr11:86229800-86231400	Enhancers	NHLF	lung
33	chr11:86229800-86231600	Enhancers	Duodenum Smooth Muscle	Duodenum
34	chr11:86229800-86231600	Enhancers	Ovary	ovary
35	chr11:86229800-86231800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr11:86229800-86231800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
37	chr11:86229800-86231800	Enhancers	Placenta Amnion	Placenta Amnion
38	chr11:86229800-86231800	Enhancers	Skeletal Muscle Female	skeletal muscle
39	chr11:86229800-86231800	Enhancers	Stomach Smooth Muscle	stomach
40	chr11:86229800-86232000	Enhancers	Breast Myoepithelial Primary Cells	Breast
41	chr11:86229800-86232000	Enhancers	A549	lung
42	chr11:86229800-86232200	Enhancers	Skeletal Muscle Male	skeletal muscle
43	chr11:86230000-86231600	Enhancers	Colon Smooth Muscle	Colon
44	chr11:86230000-86231800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr11:86230000-86234600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr11:86230200-86231200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
47	chr11:86230200-86231800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr11:86230200-86234600	Weak transcription	Stomach Mucosa	stomach
49	chr11:86230400-86231400	Enhancers	Gastric	stomach
50	chr11:86230400-86231400	Enhancers	Lung	lung

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