Variant report

Variant	rs9535248
Chromosome Location	chr13:50031610-50031611
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	chr13:50029751..50032528-chr13:50034704..50037567,2	MCF-7	breast:
2	chr13:50020031..50021593-chr13:50030911..50032935,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000215462	Chromatin interaction

Extended variants
information (count: 62 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs12050042	0.92[ASN][1000 genomes]
rs1409016	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1536194	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1543514	0.85[EUR][1000 genomes]
rs1555530	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1812	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1980794	0.92[ASN][1000 genomes]
rs1980795	0.92[ASN][1000 genomes]
rs1998782	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2057415	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2057417	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2407689	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2407692	0.84[EUR][1000 genomes]
rs3764085	0.92[ASN][1000 genomes]
rs3764090	0.83[EUR][1000 genomes]
rs3764091	0.83[EUR][1000 genomes]
rs3794381	0.90[ASN][1000 genomes]
rs4468500	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4941642	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4942831	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4942832	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6561525	0.84[EUR][1000 genomes]
rs71188363	0.86[ASN][1000 genomes]
rs7139634	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs721458	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7321670	0.85[EUR][1000 genomes]
rs7328782	0.83[EUR][1000 genomes]
rs7329078	0.83[ASN][1000 genomes]
rs7330512	0.83[EUR][1000 genomes]
rs7338755	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7982297	0.85[EUR][1000 genomes]
rs7982598	0.85[EUR][1000 genomes]
rs7987293	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7992603	0.84[EUR][1000 genomes]
rs7994115	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7994130	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7996852	0.80[EUR][1000 genomes]
rs7998022	0.83[EUR][1000 genomes]
rs7998427	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7998660	0.83[EUR][1000 genomes]
rs9316453	0.85[EUR][1000 genomes]
rs9535249	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9568219	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9568223	0.92[ASN][1000 genomes]
rs967163	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs967164	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 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	nsv430558	chr13:49914393-50059354	Active TSS Enhancers ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
3	nsv430559	chr13:49930369-50059354	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
4	nsv430560	chr13:49930643-50059354	Active TSS Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
5	nsv430562	chr13:49930643-50067246	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
6	nsv430561	chr13:49930643-50089844	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
7	nsv430564	chr13:49945247-50059354	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
8	nsv430566	chr13:49945247-50089844	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
9	nsv430571	chr13:49961137-50059354	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
10	nsv430570	chr13:49961137-50089844	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
11	esv1807924	chr13:49991885-50036730	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
12	esv1796315	chr13:49992988-50031868	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
13	nsv523648	chr13:50005444-50086266	Strong transcription Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
14	nsv561613	chr13:50013622-50086266	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
15	nsv900070	chr13:50013622-50087142	Enhancers Bivalent/Poised TSS Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
16	esv3404	chr13:50031323-50031645	Enhancers Weak transcription Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9535248	PHF11	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:92 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:50019400-50036200	Weak transcription	Esophagus	oesophagus
2	chr13:50019600-50034400	Weak transcription	Adipose Nuclei	Adipose
3	chr13:50019600-50035400	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr13:50019600-50035400	Weak transcription	Brain Substantia Nigra	brain
5	chr13:50019600-50035800	Weak transcription	Left Ventricle	heart
6	chr13:50019600-50035800	Weak transcription	HSMM	muscle
7	chr13:50019600-50036000	Weak transcription	Skeletal Muscle Female	skeletal muscle
8	chr13:50019800-50035200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr13:50019800-50035200	Weak transcription	HUES6 Cell Line	embryonic stem cell
10	chr13:50019800-50035200	Weak transcription	Primary neutrophils fromperipheralblood	blood
11	chr13:50019800-50035800	Weak transcription	Brain Cingulate Gyrus	brain
12	chr13:50019800-50035800	Weak transcription	Fetal Muscle Leg	muscle
13	chr13:50019800-50037400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr13:50019800-50037400	Weak transcription	Skeletal Muscle Male	skeletal muscle
15	chr13:50020000-50035600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr13:50020000-50035600	Weak transcription	Fetal Muscle Trunk	muscle
17	chr13:50020000-50037200	Weak transcription	Right Ventricle	heart
18	chr13:50020200-50034600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr13:50020200-50035400	Weak transcription	Placenta	Placenta
20	chr13:50020200-50035800	Weak transcription	Pancreas	Pancrea
21	chr13:50020200-50068400	Weak transcription	HMEC	breast
22	chr13:50020600-50035800	Weak transcription	Thymus	Thymus
23	chr13:50021000-50035000	Weak transcription	Rectal Mucosa Donor 31	rectum
24	chr13:50021000-50035800	Weak transcription	Fetal Intestine Small	intestine
25	chr13:50021600-50035200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
26	chr13:50021800-50035800	Weak transcription	Brain Anterior Caudate	brain
27	chr13:50022000-50032400	Weak transcription	Primary hematopoietic stem cells	blood
28	chr13:50022000-50035200	Weak transcription	Colon Smooth Muscle	Colon
29	chr13:50022000-50035600	Weak transcription	Brain Hippocampus Middle	brain
30	chr13:50022000-50035800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr13:50022000-50069000	Weak transcription	Fetal Brain Male	brain
32	chr13:50022400-50035000	Weak transcription	Fetal Heart	heart
33	chr13:50022400-50035400	Weak transcription	K562	blood
34	chr13:50023000-50068000	Weak transcription	Hela-S3	cervix
35	chr13:50024600-50034800	Weak transcription	HepG2	liver
36	chr13:50024600-50035800	Weak transcription	HSMMtube	muscle
37	chr13:50024800-50035600	Weak transcription	Osteobl	bone
38	chr13:50024800-50035800	Weak transcription	Sigmoid Colon	Sigmoid Colon
39	chr13:50024800-50035800	Weak transcription	Small Intestine	intestine
40	chr13:50027000-50034800	Weak transcription	Fetal Thymus	thymus
41	chr13:50027000-50036800	Weak transcription	A549	lung
42	chr13:50027200-50032400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
43	chr13:50027200-50032800	Weak transcription	Primary B cells from cord blood	blood
44	chr13:50027200-50035000	Weak transcription	Fetal Intestine Large	intestine
45	chr13:50027400-50032200	Weak transcription	Monocytes-CD14+_RO01746	blood
46	chr13:50027400-50034200	Weak transcription	Primary monocytes fromperipheralblood	blood
47	chr13:50027600-50035000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr13:50028000-50033600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr13:50028200-50032200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
50	chr13:50028600-50033600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood

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