Variant report

Variant	rs6592301
Chromosome Location	chr11:86318909-86318910
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:86166796..86167792-chr11:86318880..86319916,3	MCF-7	breast:
2	chr11:86316921..86319182-chr11:86528850..86531026,2	MCF-7	breast:
3	chr11:86318542..86319850-chr11:86528941..86530646,11	MCF-7	breast:
4	chr11:86232940..86235698-chr11:86318097..86321251,3	MCF-7	breast:
5	chr11:86302794..86305608-chr11:86317191..86320162,2	K562	blood:
6	chr11:86316496..86321662-chr11:86508610..86513631,11	MCF-7	breast:
7	chr11:86166955..86167789-chr11:86318883..86320001,8	MCF-7	breast:
8	chr11:86318121..86320638-chr11:86509827..86512612,4	MCF-7	breast:
9	chr11:86288660..86290609-chr11:86318150..86319919,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000150687	Chromatin interaction

Extended variants
information (count: 66 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs10792865	0.86[CHB][hapmap];0.86[JPT][hapmap]
rs11234719	1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11234731	1.00[CHB][hapmap];0.86[JPT][hapmap];0.84[ASN][1000 genomes]
rs12274942	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12282010	1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.85[TSI][hapmap];0.90[YRI][hapmap];0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12288119	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17757676	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];1.00[ASN][1000 genomes]
rs1938921	1.00[CHB][hapmap];0.93[JPT][hapmap];0.93[ASN][1000 genomes]
rs1938929	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1938931	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1938932	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1938935	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2017483	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2212340	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2212341	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4144866	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4245417	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4245418	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4245419	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4245420	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4245421	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4245422	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4245423	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4245424	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4319536	0.86[CHB][hapmap];0.86[JPT][hapmap]
rs4439535	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4592448	0.86[CHB][hapmap];0.86[JPT][hapmap]
rs4943948	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4943949	0.98[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4944602	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4944603	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4944607	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4944609	0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4944611	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4944612	0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4944618	0.85[ASN][1000 genomes]
rs496167	0.90[ASN][1000 genomes]
rs538058	0.81[CHB][hapmap]
rs550168	0.81[ASN][1000 genomes]
rs647782	0.87[ASN][1000 genomes]
rs656307	0.90[ASN][1000 genomes]
rs6592302	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs661954	0.81[CHB][hapmap]
rs663543	0.90[ASN][1000 genomes]
rs679220	0.81[CHB][hapmap]
rs7105863	0.94[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.88[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7106865	0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.86[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs7115580	0.95[CEU][hapmap];0.95[YRI][hapmap];0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7115594	0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7115834	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7120444	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7123044	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7937853	0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7941337	0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7941446	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7948981	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7951868	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9787905	0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs999472	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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	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
4	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
5	nsv898057	chr11:86306401-86335459	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv522823	chr11:86317519-86321576	Weak transcription Enhancers Active TSS Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	nsv525957	chr11:86318892-86318909	Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6592301	CTSC	cis	cerebellum	SCAN

Chromatin state (count:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:86308800-86321600	Weak transcription	Left Ventricle	heart
2	chr11:86309400-86321600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr11:86315600-86319000	Weak transcription	Fetal Intestine Large	intestine
4	chr11:86316200-86320200	Enhancers	HUVEC	blood vessel
5	chr11:86316400-86320400	Enhancers	Fetal Stomach	stomach
6	chr11:86316800-86319600	Enhancers	Fetal Brain Male	brain
7	chr11:86317000-86319000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr11:86317000-86319000	Enhancers	Right Ventricle	heart
9	chr11:86317000-86319200	Enhancers	Stomach Smooth Muscle	stomach
10	chr11:86317000-86319200	Enhancers	A549	lung
11	chr11:86317000-86319600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr11:86317000-86319600	Enhancers	Ovary	ovary
13	chr11:86317000-86319800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr11:86317000-86320200	Enhancers	Fetal Heart	heart
15	chr11:86317200-86319000	Enhancers	Colon Smooth Muscle	Colon
16	chr11:86317200-86319200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr11:86317200-86319200	Enhancers	Skeletal Muscle Female	skeletal muscle
18	chr11:86317200-86319800	Enhancers	Fetal Muscle Leg	muscle
19	chr11:86317200-86320400	Enhancers	Rectal Smooth Muscle	rectum
20	chr11:86317200-86320400	Enhancers	Hela-S3	cervix
21	chr11:86317400-86319200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr11:86317400-86319600	Enhancers	Aorta	Aorta
23	chr11:86317400-86319600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
24	chr11:86317400-86320000	Enhancers	Muscle Satellite Cultured Cells	--
25	chr11:86317400-86320000	Enhancers	HSMM	muscle
26	chr11:86317400-86320000	Enhancers	NH-A	brain
27	chr11:86317400-86320000	Enhancers	NHDF-Ad	bronchial
28	chr11:86317400-86320200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr11:86317400-86321600	Weak transcription	Pancreas	Pancrea
30	chr11:86317600-86319200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr11:86317600-86319600	Enhancers	ES-I3 Cell Line	embryonic stem cell
32	chr11:86317600-86320000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr11:86317600-86320000	Enhancers	Duodenum Smooth Muscle	Duodenum
34	chr11:86317600-86320000	Enhancers	NHEK	skin
35	chr11:86317600-86320000	Enhancers	Osteobl	bone
36	chr11:86317800-86319600	Enhancers	Rectal Mucosa Donor 31	rectum
37	chr11:86317800-86320000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr11:86317800-86320600	Enhancers	Breast Myoepithelial Primary Cells	Breast
39	chr11:86317800-86320600	Enhancers	HMEC	breast
40	chr11:86318000-86319200	Weak transcription	Adipose Nuclei	Adipose
41	chr11:86318000-86319400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
42	chr11:86318000-86319400	Weak transcription	Pancreatic Islets	Pancreatic Islet
43	chr11:86318000-86319600	Enhancers	Fetal Kidney	kidney
44	chr11:86318000-86320000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr11:86318200-86319000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
46	chr11:86318200-86319200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr11:86318200-86319600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr11:86318200-86321200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
49	chr11:86318400-86319000	Weak transcription	Stomach Mucosa	stomach
50	chr11:86318400-86319400	Weak transcription	HUES6 Cell Line	embryonic stem cell

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