Variant report

Variant	rs2512996
Chromosome Location	chr11:86446483-86446484
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:86438833..86441351-chr11:86445320..86447426,4	MCF-7	breast:
2	chr11:86445788..86450763-chr11:86452280..86455324,5	K562	blood:
3	chr11:86445700..86450143-chr11:86450733..86453676,4	MCF-7	breast:
4	chr11:86382791..86384819-chr11:86445397..86448151,2	MCF-7	breast:
5	chr11:86445661..86448422-chr11:86500757..86504196,4	MCF-7	breast:
6	chr11:86446334..86448722-chr11:86490852..86493629,3	MCF-7	breast:
7	chr11:86445705..86457398-chr11:86504607..86518485,46	MCF-7	breast:

Variant related genes	Relation type
ENSG00000151376	Chromatin interaction
ENSG00000150687	Chromatin interaction

Extended variants
information (count: 64 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs1075702	0.95[CHB][hapmap];0.85[CHD][hapmap];0.82[MEX][hapmap];0.84[ASN][1000 genomes]
rs11234783	0.82[ASN][1000 genomes]
rs12802848	0.81[CHB][hapmap]
rs2433406	0.95[CHB][hapmap];0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs2433407	0.91[CHB][hapmap];0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs2433408	0.95[CHB][hapmap];0.87[JPT][hapmap];0.84[ASN][1000 genomes]
rs2433409	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2433410	0.91[ASN][1000 genomes]
rs2433411	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2433424	0.94[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs2433425	0.95[ASN][1000 genomes]
rs2433426	1.00[CEU][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2433427	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2433428	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2433429	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2433430	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2433431	0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.86[MKK][hapmap];0.82[YRI][hapmap];0.96[ASN][1000 genomes]
rs2433432	0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.86[MKK][hapmap];0.82[YRI][hapmap];0.95[ASN][1000 genomes]
rs2433433	0.91[CHB][hapmap];0.85[CHD][hapmap];0.83[ASN][1000 genomes]
rs2433434	0.91[CHB][hapmap];0.87[CHD][hapmap];0.83[ASN][1000 genomes]
rs2433435	0.95[CHB][hapmap];0.90[CHD][hapmap];0.83[ASN][1000 genomes]
rs2433436	0.91[CHB][hapmap];0.90[CHD][hapmap];0.82[ASN][1000 genomes]
rs2433438	0.91[CHB][hapmap];0.87[CHD][hapmap];0.83[ASN][1000 genomes]
rs2433439	0.91[CHB][hapmap];0.90[CHD][hapmap];0.83[ASN][1000 genomes]
rs2433440	0.82[ASN][1000 genomes]
rs2433441	0.82[ASN][1000 genomes]
rs2512978	0.82[ASN][1000 genomes]
rs2512979	0.82[ASN][1000 genomes]
rs2512997	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2512998	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2512999	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2513000	0.96[ASN][1000 genomes]
rs2513001	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2513003	0.95[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2513005	0.86[CHB][hapmap]
rs2513006	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2513008	0.92[ASN][1000 genomes]
rs2513009	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2513010	0.92[ASN][1000 genomes]
rs2513011	0.91[ASN][1000 genomes]
rs2513012	0.91[ASN][1000 genomes]
rs2513018	0.95[CHB][hapmap];0.83[ASN][1000 genomes]
rs3096711	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3096714	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3096715	0.95[CHB][hapmap];0.83[ASN][1000 genomes]
rs3096716	0.86[CHB][hapmap];0.82[ASN][1000 genomes]
rs4245426	0.84[ASN][1000 genomes]
rs4307743	0.81[CHB][hapmap]
rs4570601	0.81[CHB][hapmap]
rs4586194	0.94[ASN][1000 genomes]
rs4943957	0.82[ASN][1000 genomes]
rs4944630	0.81[CHB][hapmap]
rs7108176	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7108300	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7124794	0.94[ASN][1000 genomes]
rs7129902	0.89[ASN][1000 genomes]
rs7948063	0.81[CHB][hapmap]
rs7951582	0.81[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2512996	CCDC83	cis	parietal	SCAN

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:86407000-86451600	Weak transcription	Left Ventricle	heart
2	chr11:86424200-86449800	Weak transcription	Pancreas	Pancrea
3	chr11:86440000-86446600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr11:86444400-86447400	Enhancers	Hela-S3	cervix
5	chr11:86446000-86446600	Enhancers	NHDF-Ad	bronchial
6	chr11:86446000-86446800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr11:86446000-86447200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr11:86446000-86448000	Flanking Active TSS	A549	lung
9	chr11:86446000-86451600	Enhancers	NHLF	lung
10	chr11:86446000-86451800	Enhancers	HUVEC	blood vessel
11	chr11:86446000-86452000	Enhancers	HSMM	muscle
12	chr11:86446000-86458000	Enhancers	HMEC	breast
13	chr11:86446200-86446800	Genic enhancers	Fetal Kidney	kidney
14	chr11:86446200-86447200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr11:86446200-86448000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
16	chr11:86446200-86448600	Enhancers	Fetal Brain Male	brain
17	chr11:86446200-86452000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr11:86446200-86452000	Enhancers	NH-A	brain
19	chr11:86446200-86452000	Enhancers	Osteobl	bone
20	chr11:86446200-86453200	Enhancers	Fetal Lung	lung
21	chr11:86446400-86446800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr11:86446400-86447000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr11:86446400-86447200	Enhancers	NHEK	skin
24	chr11:86446400-86447400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr11:86446400-86447400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr11:86446400-86447800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr11:86446400-86448200	Enhancers	Fetal Brain Female	brain
28	chr11:86446400-86448400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr11:86446400-86449000	Enhancers	HSMMtube	muscle
30	chr11:86446400-86455200	Enhancers	Fetal Adrenal Gland	Adrenal Gland

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