Variant report

Variant	rs10767612
Chromosome Location	chr11:3827301-3827302
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:3818014..3819859-chr11:3826407..3829369,2	MCF-7	breast:
2	chr11:3816139..3821205-chr11:3826361..3831544,11	MCF-7	breast:

Variant related genes	Relation type
ENSG00000110713	Chromatin interaction
ENSG00000148985	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs1037382	0.95[CEU][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1037383	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1037384	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10742170	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10767605	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10767606	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10767619	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10835113	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10835117	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10835147	0.89[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs11029824	0.84[EUR][1000 genomes]
rs11029828	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11029830	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11029831	0.83[AMR][1000 genomes]
rs11029836	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11602563	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12576671	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1530892	0.93[ASN][1000 genomes]
rs1530893	0.86[ASN][1000 genomes]
rs2278845	0.86[JPT][hapmap]
rs2412290	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2898936	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2898938	0.94[ASW][hapmap];1.00[CEU][hapmap];0.83[CHB][hapmap];0.83[CHD][hapmap];0.87[GIH][hapmap];0.81[JPT][hapmap];0.89[LWK][hapmap];0.96[MEX][hapmap];0.85[MKK][hapmap];0.92[TSI][hapmap];0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3781615	1.00[CEU][hapmap];0.94[CHB][hapmap];0.83[CHD][hapmap];0.94[GIH][hapmap];0.81[JPT][hapmap];0.91[MEX][hapmap];0.92[TSI][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4910829	0.87[ASN][1000 genomes]
rs4910845	0.81[ASN][1000 genomes]
rs7117291	0.94[ASN][1000 genomes]
rs7120836	0.94[ASW][hapmap];0.91[MEX][hapmap];0.85[MKK][hapmap];0.81[AMR][1000 genomes]
rs7479058	0.89[ASN][1000 genomes]
rs7946577	0.94[ASW][hapmap];0.90[CEU][hapmap];0.89[CHB][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.91[MEX][hapmap];0.92[TSI][hapmap];0.94[YRI][hapmap];0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9733994	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9737461	0.90[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	nsv1049560	chr11:3678259-3980746	Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	nsv540907	chr11:3678259-3980746	Weak transcription Active TSS Enhancers Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
3	nsv1052744	chr11:3739162-4017601	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
4	nsv1047025	chr11:3750969-4017601	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
5	esv1803195	chr11:3806490-3924156	Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
6	nsv1046065	chr11:3808818-4049150	Active TSS Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
7	nsv540909	chr11:3808818-4049150	Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
8	nsv1038220	chr11:3818041-3860024	Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs10767612	PPFIBP2	cis	cerebellum	SCAN
rs10767612	OR56A1	cis	parietal	SCAN
rs10767612	OR52E2	cis	cerebellum	SCAN
rs10767612	TMEM80	cis	cerebellum	SCAN
rs10767612	IFITM3	cis	cerebellum	SCAN
rs10767612	SMPD1	cis	cerebellum	SCAN

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:3818800-3829000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr11:3819600-3828800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr11:3819600-3828800	Weak transcription	Fetal Kidney	kidney
4	chr11:3819600-3829000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr11:3819600-3829000	Weak transcription	Primary T cells from cord blood	blood
6	chr11:3819600-3829000	Weak transcription	Stomach Mucosa	stomach
7	chr11:3819800-3828800	Weak transcription	Primary hematopoietic stem cells	blood
8	chr11:3819800-3828800	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr11:3819800-3828800	Weak transcription	Rectal Mucosa Donor 29	rectum
10	chr11:3819800-3829000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
11	chr11:3819800-3829000	Weak transcription	Brain Angular Gyrus	brain
12	chr11:3819800-3829000	Weak transcription	Duodenum Smooth Muscle	Duodenum
13	chr11:3819800-3829000	Weak transcription	Thymus	Thymus
14	chr11:3820200-3829000	Weak transcription	Primary T helper cells PMA-I stimulated	--
15	chr11:3820200-3829000	Weak transcription	Fetal Muscle Leg	muscle
16	chr11:3820400-3828800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
17	chr11:3820400-3828800	Weak transcription	Hela-S3	cervix
18	chr11:3820600-3828800	Weak transcription	Primary T cells fromperipheralblood	blood
19	chr11:3823800-3828600	Weak transcription	Dnd41	blood
20	chr11:3823800-3828800	Weak transcription	HepG2	liver
21	chr11:3823800-3829000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr11:3823800-3829000	Weak transcription	Duodenum Mucosa	Duodenum
23	chr11:3823800-3829200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr11:3824000-3828800	Weak transcription	K562	blood
25	chr11:3824000-3829000	Weak transcription	Fetal Intestine Large	intestine
26	chr11:3824000-3829000	Weak transcription	Fetal Stomach	stomach
27	chr11:3824000-3829000	Weak transcription	Rectal Mucosa Donor 31	rectum
28	chr11:3824000-3829000	Weak transcription	A549	lung
29	chr11:3824000-3829200	Weak transcription	HSMMtube	muscle
30	chr11:3824200-3829000	Weak transcription	Fetal Intestine Small	intestine
31	chr11:3825800-3829000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr11:3825800-3829000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr11:3825800-3829000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr11:3825800-3829000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr11:3825800-3829000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr11:3825800-3829000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr11:3825800-3829000	Weak transcription	HUVEC	blood vessel
38	chr11:3825800-3829000	Weak transcription	NH-A	brain
39	chr11:3825800-3829000	Weak transcription	NHDF-Ad	bronchial
40	chr11:3825800-3829200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr11:3825800-3829200	Weak transcription	HMEC	breast
42	chr11:3825800-3829200	Weak transcription	HSMM	muscle
43	chr11:3825800-3829200	Weak transcription	NHEK	skin
44	chr11:3825800-3829200	Weak transcription	Osteobl	bone
45	chr11:3826000-3828800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr11:3826000-3829000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr11:3826000-3829000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr11:3826000-3829200	Weak transcription	Muscle Satellite Cultured Cells	--
49	chr11:3826200-3829000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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