Variant report

Variant	rs55854833
Chromosome Location	chr11:67329741-67329742
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	chr11:67329340..67331147-chr11:67336004..67337514,2	MCF-7	breast:

Extended variants
information (count: 43 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs1079719	0.84[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs10896181	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11605586	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17593068	0.89[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2370141	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2370142	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2370143	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs36211089	0.82[EUR][1000 genomes]
rs4930436	0.94[EUR][1000 genomes]
rs58046082	0.86[EUR][1000 genomes]
rs6591249	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6591251	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6591252	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6591254	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6591255	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6591256	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7103713	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7106423	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7106675	0.89[EUR][1000 genomes]
rs7108426	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs762803	0.87[AFR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7927657	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7940813	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7941395	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7941648	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7945035	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7945927	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7948478	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7948823	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7948911	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7949394	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7949587	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7952081	0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531397	chr11:66653381-67465721	Active TSS Enhancers Strong transcription Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	271 gene(s)	inside rSNPs	diseases
2	nsv1043037	chr11:67027193-67357425	Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Weak transcription Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	213 gene(s)	inside rSNPs	diseases
3	nsv897801	chr11:67033076-67432479	Bivalent Enhancer Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	236 gene(s)	inside rSNPs	diseases
4	nsv897807	chr11:67155210-67414492	Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	176 gene(s)	inside rSNPs	diseases
5	nsv897808	chr11:67155210-67419855	Flanking Active TSS Strong transcription Enhancers Weak transcription Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	176 gene(s)	inside rSNPs	diseases
6	nsv534229	chr11:67164667-67411909	Flanking Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	175 gene(s)	inside rSNPs	diseases
7	esv2422195	chr11:67234322-67626901	Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	146 gene(s)	inside rSNPs	diseases
8	nsv1041988	chr11:67319916-67749246	Enhancers Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
9	esv3470896	chr11:67329714-67332724	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
10	nsv555257	chr11:67329742-67331278	Weak transcription Enhancers Flanking Active TSS	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs55854833	PTPRCAP	cis	Adipose Subcutaneous	GTEx
rs55854833	PTPRCAP	cis	Nerve Tibial	GTEx

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:67324200-67331000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr11:67325600-67331600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr11:67326000-67330800	Weak transcription	Left Ventricle	heart
4	chr11:67326400-67329800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr11:67326400-67329800	Weak transcription	NHEK	skin
6	chr11:67326400-67330400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr11:67326400-67330400	Weak transcription	Psoas Muscle	Psoas
8	chr11:67326400-67330600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr11:67326400-67330600	Weak transcription	Skeletal Muscle Female	skeletal muscle
10	chr11:67326400-67330800	Weak transcription	Right Atrium	heart
11	chr11:67326400-67331000	Weak transcription	Pancreas	Pancrea
12	chr11:67326400-67332200	Enhancers	Fetal Intestine Large	intestine
13	chr11:67326600-67332200	Enhancers	Fetal Intestine Small	intestine
14	chr11:67326800-67330000	Weak transcription	Fetal Muscle Trunk	muscle
15	chr11:67327000-67330800	Weak transcription	Rectal Mucosa Donor 31	rectum
16	chr11:67327200-67330400	Weak transcription	Skeletal Muscle Male	skeletal muscle
17	chr11:67327200-67330400	Weak transcription	HSMMtube	muscle
18	chr11:67327200-67330400	Weak transcription	Osteobl	bone
19	chr11:67327200-67330600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr11:67327200-67330600	Weak transcription	Fetal Muscle Leg	muscle
21	chr11:67327200-67330600	Weak transcription	Stomach Mucosa	stomach
22	chr11:67327200-67331000	Weak transcription	Right Ventricle	heart
23	chr11:67327600-67330800	Weak transcription	Aorta	Aorta
24	chr11:67328000-67330200	Weak transcription	HUVEC	blood vessel
25	chr11:67328400-67330600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
26	chr11:67328600-67330200	Enhancers	Primary B cells from peripheral blood	blood
27	chr11:67328600-67333800	Enhancers	Placenta	Placenta
28	chr11:67329000-67330200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
29	chr11:67329000-67332200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr11:67329200-67330800	Enhancers	HepG2	liver
31	chr11:67329200-67331400	Enhancers	Liver	Liver
32	chr11:67329400-67330000	Enhancers	Primary T helper cells PMA-I stimulated	--
33	chr11:67329400-67330000	Flanking Active TSS	GM12878-XiMat	blood
34	chr11:67329400-67330600	Enhancers	A549	lung
35	chr11:67329400-67332000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr11:67329400-67332000	Enhancers	Fetal Heart	heart
37	chr11:67329600-67330000	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
38	chr11:67329600-67330400	Weak transcription	Fetal Kidney	kidney
39	chr11:67329600-67330800	Enhancers	Hela-S3	cervix
40	chr11:67329600-67331000	Enhancers	Muscle Satellite Cultured Cells	--

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