Variant report

Variant	rs2433439
Chromosome Location	chr11:86456526-86456527
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:86454835..86456464-chr11:86456517..86458512,2	K562	blood:
2	chr11:86429172..86438482-chr11:86450202..86456550,9	MCF-7	breast:
3	chr11:86404739..86407323-chr11:86454974..86456802,2	MCF-7	breast:
4	chr11:86456277..86457862-chr11:86528085..86530264,2	MCF-7	breast:
5	chr11:86381743..86384128-chr11:86455249..86457298,2	MCF-7	breast:
6	chr11:86445705..86457398-chr11:86504607..86518485,46	MCF-7	breast:

Variant related genes	Relation type
ENSG00000151376	Chromatin interaction
ENSG00000150687	Chromatin interaction
ENSG00000255250	Chromatin interaction

Extended variants
information (count: 72 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs1075702	0.95[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs11234783	0.91[ASN][1000 genomes]
rs11601553	0.86[JPT][hapmap]
rs12420039	0.86[MEX][hapmap]
rs12576018	0.83[ASN][1000 genomes]
rs12802848	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs17211787	0.93[MEX][hapmap]
rs17211926	0.86[CHB][hapmap];0.86[JPT][hapmap]
rs17819068	0.86[CHB][hapmap];0.86[JPT][hapmap]
rs17819187	0.86[MEX][hapmap]
rs1939111	0.86[MEX][hapmap]
rs2005192	0.82[CHB][hapmap]
rs2433406	0.86[CHB][hapmap]
rs2433407	0.91[CHB][hapmap]
rs2433408	0.86[CHB][hapmap]
rs2433409	0.91[CHB][hapmap];0.84[CHD][hapmap]
rs2433424	0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2433426	0.80[ASN][1000 genomes]
rs2433427	0.91[CHB][hapmap]
rs2433428	0.82[ASN][1000 genomes]
rs2433429	0.91[CHB][hapmap];0.87[CHD][hapmap];0.82[ASN][1000 genomes]
rs2433431	0.95[CHB][hapmap];0.90[CHD][hapmap];0.93[MEX][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2433432	0.95[CHB][hapmap];0.90[CHD][hapmap];0.93[MEX][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2433433	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.86[TSI][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2433434	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.82[MKK][hapmap];0.86[TSI][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2433435	0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2433436	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs2433438	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2433440	0.99[ASN][1000 genomes]
rs2433441	0.99[ASN][1000 genomes]
rs2512978	0.99[ASN][1000 genomes]
rs2512979	0.99[ASN][1000 genomes]
rs2512996	0.91[CHB][hapmap];0.90[CHD][hapmap];0.83[ASN][1000 genomes]
rs2512997	0.91[CHB][hapmap];0.90[CHD][hapmap];0.83[ASN][1000 genomes]
rs2512999	0.81[ASN][1000 genomes]
rs2513000	0.83[ASN][1000 genomes]
rs2513001	0.83[ASN][1000 genomes]
rs2513003	0.95[CHB][hapmap];0.84[CHD][hapmap];0.93[MEX][hapmap];0.83[ASN][1000 genomes]
rs2513004	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2513005	0.95[CHB][hapmap];0.91[JPT][hapmap];0.90[ASN][1000 genomes]
rs2513018	0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2513019	0.80[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs3096715	0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs3096716	0.95[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs3096717	0.94[ASN][1000 genomes]
rs3096718	0.88[ASN][1000 genomes]
rs3809048	0.93[MEX][hapmap]
rs4128368	0.86[CHB][hapmap];0.86[JPT][hapmap];0.86[MEX][hapmap]
rs4245426	0.93[ASN][1000 genomes]
rs4269941	0.86[CHB][hapmap];0.86[JPT][hapmap];0.86[MEX][hapmap]
rs4304806	0.86[MEX][hapmap]
rs4307743	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs4423210	0.85[MEX][hapmap]
rs4495915	0.82[CEU][hapmap]
rs4570601	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs4586194	0.81[ASN][1000 genomes]
rs4943957	0.91[ASN][1000 genomes]
rs4944629	0.88[ASN][1000 genomes]
rs4944630	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs6592315	0.81[JPT][hapmap]
rs7124794	0.80[ASN][1000 genomes]
rs7126492	0.86[JPT][hapmap]
rs7948063	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs7951582	0.82[CHB][hapmap];0.86[JPT][hapmap]

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	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	nsv1055071	chr11:86301240-86465465	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv428263	chr11:86357990-86508480	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv1049157	chr11:86409059-86504155	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
6	nsv521505	chr11:86438115-86515072	Weak transcription Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
7	nsv468775	chr11:86453415-86480716	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS	Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
8	nsv555705	chr11:86453415-86480716	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS	Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2433439	PRCP	cis	cerebellum	SCAN
rs2433439	CCDC83	cis	parietal	SCAN

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:86446000-86458000	Enhancers	HMEC	breast
2	chr11:86450200-86459800	Enhancers	Placenta Amnion	Placenta Amnion
3	chr11:86452200-86458000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr11:86452400-86457600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr11:86453000-86457600	Weak transcription	Fetal Heart	heart
6	chr11:86453400-86459200	Weak transcription	Brain Anterior Caudate	brain
7	chr11:86453400-86459600	Weak transcription	Fetal Muscle Trunk	muscle
8	chr11:86453800-86459200	Weak transcription	Ovary	ovary
9	chr11:86454000-86474000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr11:86454400-86456600	Weak transcription	Psoas Muscle	Psoas
11	chr11:86454400-86457600	Weak transcription	Lung	lung
12	chr11:86454400-86459200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr11:86454800-86460600	Weak transcription	Adipose Nuclei	Adipose
14	chr11:86455000-86457400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr11:86455000-86457800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr11:86455000-86460400	Weak transcription	Rectal Smooth Muscle	rectum
17	chr11:86455000-86461000	Weak transcription	Fetal Lung	lung
18	chr11:86455000-86461200	Enhancers	Osteobl	bone
19	chr11:86455000-86461600	Enhancers	NHDF-Ad	bronchial
20	chr11:86455000-86462400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr11:86455200-86456600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr11:86455200-86457400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr11:86455200-86457400	Weak transcription	Fetal Stomach	stomach
24	chr11:86455200-86458000	Enhancers	Hela-S3	cervix
25	chr11:86455200-86458000	Weak transcription	NHLF	lung
26	chr11:86455200-86459000	Weak transcription	Stomach Smooth Muscle	stomach
27	chr11:86455200-86460600	Enhancers	Muscle Satellite Cultured Cells	--
28	chr11:86455200-86460800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr11:86455200-86464600	Weak transcription	Duodenum Smooth Muscle	Duodenum
30	chr11:86455400-86456600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr11:86455400-86456600	Weak transcription	HSMMtube	muscle
32	chr11:86455400-86456600	Weak transcription	NHEK	skin
33	chr11:86455400-86457200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr11:86455400-86457200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr11:86455800-86456800	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr11:86456000-86456600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr11:86456000-86456800	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr11:86456200-86456600	Enhancers	Aorta	Aorta
39	chr11:86456200-86456800	Weak transcription	A549	lung
40	chr11:86456200-86459800	Enhancers	NH-A	brain
41	chr11:86456200-86462400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr11:86456400-86456600	Enhancers	Esophagus	oesophagus
43	chr11:86456400-86456800	Enhancers	Skeletal Muscle Female	skeletal muscle
44	chr11:86456400-86457200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr11:86456400-86457200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
46	chr11:86456400-86458200	Enhancers	Breast Myoepithelial Primary Cells	Breast
47	chr11:86456400-86461400	Enhancers	HSMM	muscle

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