Variant report

Variant	rs7139634
Chromosome Location	chr13:50063687-50063688
allele	A/C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:50061049..50067624-chr13:50068104..50073631,8	MCF-7	breast:

Variant related genes	Relation type
ENSG00000136147	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs12050042	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1409016	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1536194	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1555530	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1812	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1980794	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1980795	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1998782	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2057413	0.83[EUR][1000 genomes]
rs2057415	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2057417	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2407689	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3764085	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3794381	0.94[ASN][1000 genomes]
rs4142285	0.83[EUR][1000 genomes]
rs4468500	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4941642	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4942831	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4942832	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs71188363	0.90[ASN][1000 genomes]
rs721458	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7321228	0.83[EUR][1000 genomes]
rs7329078	0.88[ASN][1000 genomes]
rs7338755	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7987293	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7994115	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7994130	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7996852	0.83[EUR][1000 genomes]
rs7998427	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9526564	0.83[EUR][1000 genomes]
rs9535248	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9535249	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9568219	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9568223	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs959421	0.83[EUR][1000 genomes]
rs967163	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs967164	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 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	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
3	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
4	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
5	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
6	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
7	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
8	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
9	nsv561614	chr13:50042983-50086253	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
10	nsv561615	chr13:50042983-50086266	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
11	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7139634	PHF11	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:50020200-50068400	Weak transcription	HMEC	breast
2	chr13:50022000-50069000	Weak transcription	Fetal Brain Male	brain
3	chr13:50023000-50068000	Weak transcription	Hela-S3	cervix
4	chr13:50031800-50068800	Weak transcription	Psoas Muscle	Psoas
5	chr13:50034400-50068800	Weak transcription	NH-A	brain
6	chr13:50036400-50068600	Weak transcription	Stomach Mucosa	stomach
7	chr13:50036600-50068000	Weak transcription	K562	blood
8	chr13:50037800-50064000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr13:50037800-50068400	Weak transcription	HUVEC	blood vessel
10	chr13:50037800-50069000	Weak transcription	Colonic Mucosa	Colon
11	chr13:50038000-50063800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
12	chr13:50038000-50068800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr13:50038400-50066800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr13:50038400-50066800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr13:50038400-50069000	Weak transcription	H1 Cell Line	embryonic stem cell
16	chr13:50038400-50069400	Weak transcription	Small Intestine	intestine
17	chr13:50038600-50068800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr13:50038800-50069000	Weak transcription	HSMM	muscle
19	chr13:50039000-50068200	Weak transcription	Muscle Satellite Cultured Cells	--
20	chr13:50039200-50068800	Weak transcription	Cortex derived primary cultured neurospheres	brain
21	chr13:50039400-50069200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr13:50040600-50064800	Weak transcription	HUES64 Cell Line	embryonic stem cell
23	chr13:50041000-50068800	Weak transcription	Pancreatic Islets	Pancreatic Islet
24	chr13:50041400-50069400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr13:50041600-50063800	Strong transcription	Primary T helper cells PMA-I stimulated	--
26	chr13:50042200-50067000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
27	chr13:50049400-50069000	Weak transcription	HUES6 Cell Line	embryonic stem cell
28	chr13:50051200-50068400	Weak transcription	NHLF	lung
29	chr13:50051400-50069000	Weak transcription	Fetal Brain Female	brain
30	chr13:50051400-50069400	Weak transcription	Gastric	stomach
31	chr13:50051600-50068400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
32	chr13:50051800-50068800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
33	chr13:50052000-50068800	Weak transcription	HUES48 Cell Line	embryonic stem cell
34	chr13:50052200-50069200	Weak transcription	Brain Germinal Matrix	brain
35	chr13:50052600-50069000	Weak transcription	Placenta	Placenta
36	chr13:50052600-50069200	Weak transcription	Brain Angular Gyrus	brain
37	chr13:50053000-50068600	Weak transcription	Skeletal Muscle Male	skeletal muscle
38	chr13:50053000-50069200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr13:50053000-50069400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr13:50053000-50069400	Weak transcription	Esophagus	oesophagus
41	chr13:50053000-50069400	Weak transcription	Spleen	Spleen
42	chr13:50053400-50069200	Weak transcription	Brain Substantia Nigra	brain
43	chr13:50055000-50067400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr13:50055400-50068600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr13:50055400-50069000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
46	chr13:50056000-50068400	Weak transcription	Rectal Smooth Muscle	rectum
47	chr13:50056400-50068000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr13:50056400-50068000	Weak transcription	NHEK	skin
49	chr13:50056400-50068400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr13:50057200-50069200	Weak transcription	Colon Smooth Muscle	Colon

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