Variant report

Variant	rs6561538
Chromosome Location	chr13:50104040-50104041
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	chr13:50100974..50104825-chr13:50157801..50160843,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000136144	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs1046027	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1046028	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1046295	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1062979	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17073051	0.88[AFR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2980	0.88[AFR][1000 genomes];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2981	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3033	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3186012	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3186013	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3186024	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs36075670	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3829366	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4942836	0.81[ASN][1000 genomes]
rs4942838	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4942839	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4942840	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6561534	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6561536	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs67307832	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7139494	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7317982	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7322077	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7323493	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7323716	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7331262	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7331330	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7337718	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7339167	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7988427	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7989504	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7990988	0.83[EUR][1000 genomes]
rs7991031	0.82[EUR][1000 genomes]
rs7995684	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7996994	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs942870	0.80[EUR][1000 genomes]
rs9535254	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9535255	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9535256	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9535257	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9535258	0.82[EUR][1000 genomes]

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	nsv1047311	chr13:49895019-50224227	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats 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 miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv916093	chr13:50050919-50290245	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv1036135	chr13:50071310-50183103	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Genic enhancers 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 target site	9 gene(s)	inside rSNPs	diseases
4	nsv541770	chr13:50071310-50183103	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
5	nsv1054965	chr13:50102730-50251347	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers 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 target site	23 gene(s)	inside rSNPs	diseases
6	nsv541771	chr13:50102730-50251347	Enhancers Active TSS Genic enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6561538	PHF11	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:50075000-50143800	Weak transcription	Small Intestine	intestine
2	chr13:50077600-50114000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr13:50080000-50107000	Weak transcription	HUES6 Cell Line	embryonic stem cell
4	chr13:50080200-50104600	Strong transcription	Primary T helper cells fromperipheralblood	blood
5	chr13:50080600-50104600	Strong transcription	Primary T cells fromperipheralblood	blood
6	chr13:50084000-50104800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
7	chr13:50084800-50104200	Strong transcription	GM12878-XiMat	blood
8	chr13:50085400-50104800	Strong transcription	Primary T helper cells PMA-I stimulated	--
9	chr13:50086400-50113600	Weak transcription	Brain Angular Gyrus	brain
10	chr13:50086600-50106200	Strong transcription	Fetal Thymus	thymus
11	chr13:50086600-50108800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr13:50086600-50114200	Weak transcription	Fetal Brain Female	brain
13	chr13:50088200-50113600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr13:50088400-50151000	Weak transcription	Psoas Muscle	Psoas
15	chr13:50088600-50134200	Weak transcription	Stomach Mucosa	stomach
16	chr13:50089200-50107400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr13:50089400-50114200	Weak transcription	Colon Smooth Muscle	Colon
18	chr13:50090000-50113600	Weak transcription	Skeletal Muscle Male	skeletal muscle
19	chr13:50090000-50122800	Weak transcription	Ovary	ovary
20	chr13:50090000-50123600	Weak transcription	Esophagus	oesophagus
21	chr13:50090200-50114200	Weak transcription	Aorta	Aorta
22	chr13:50090200-50117800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr13:50090400-50106600	Weak transcription	Rectal Smooth Muscle	rectum
24	chr13:50090400-50113400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
25	chr13:50090400-50114200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr13:50090800-50104200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr13:50091000-50114200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
28	chr13:50091400-50138800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
29	chr13:50091800-50107600	Weak transcription	Brain Inferior Temporal Lobe	brain
30	chr13:50092000-50108000	Weak transcription	Brain Cingulate Gyrus	brain
31	chr13:50092000-50112200	Weak transcription	Cortex derived primary cultured neurospheres	brain
32	chr13:50092000-50114200	Weak transcription	Fetal Brain Male	brain
33	chr13:50092200-50105400	Weak transcription	HUES48 Cell Line	embryonic stem cell
34	chr13:50092200-50105800	Weak transcription	HUES64 Cell Line	embryonic stem cell
35	chr13:50092200-50113400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr13:50093000-50108000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr13:50093800-50113400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
38	chr13:50094000-50112000	Weak transcription	HSMMtube	muscle
39	chr13:50094000-50114200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
40	chr13:50094200-50107800	Weak transcription	HepG2	liver
41	chr13:50094600-50113600	Weak transcription	Gastric	stomach
42	chr13:50094600-50113800	Weak transcription	Pancreas	Pancrea
43	chr13:50094600-50120000	Weak transcription	Spleen	Spleen
44	chr13:50094600-50141600	Weak transcription	Right Ventricle	heart
45	chr13:50095000-50120400	Weak transcription	A549	lung
46	chr13:50096000-50108000	Weak transcription	Lung	lung
47	chr13:50096600-50106800	Weak transcription	Fetal Kidney	kidney
48	chr13:50096800-50104200	Weak transcription	Fetal Intestine Large	intestine
49	chr13:50097600-50113600	Weak transcription	Sigmoid Colon	Sigmoid Colon
50	chr13:50097600-50114000	Weak transcription	Fetal Lung	lung

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