Variant report

Variant	rs4925054
Chromosome Location	chr17:19801417-19801418
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr17:19800633-19801494	U87	brain:	n/a	n/a
2	POLR2A	chr17:19801151-19801660	SK-N-SH	brain:	n/a	n/a
3	TBP	chr17:19801315-19801656	Hela-S3	cervix:	n/a	n/a
4	POLR2A	chr17:19799931-19805138	K562	blood:	n/a	n/a
5	MAX	chr17:19801301-19801668	Hela-S3	cervix:	n/a	n/a
6	RCOR1	chr17:19801183-19801758	Hela-S3	cervix:	n/a	n/a
7	POLR2A	chr17:19800354-19801678	Hela-S3	cervix:	n/a	n/a
8	USF2	chr17:19800438-19801800	Hela-S3	cervix:	n/a	n/a
9	STAT3	chr17:19801337-19801661	MCF10A-Er-Src	breast:	n/a	n/a
10	POLR2A	chr17:19801289-19801515	Hela-S3	cervix:	n/a	n/a
11	STAT3	chr17:19801343-19801661	MCF10A-Er-Src	breast:	n/a	n/a
12	GATA3	chr17:19801074-19801744	SK-N-SH	brain:	n/a	n/a
13	POLR2A	chr17:19801054-19801504	GM12892	blood:	n/a	n/a
14	PBX3	chr17:19801160-19801768	SK-N-SH	brain:	n/a	n/a
15	EP300	chr17:19801305-19801677	Hela-S3	cervix:	n/a	chr17:19801487-19801496
16	FOS	chr17:19801247-19801674	MCF10A-Er-Src	breast:	n/a	chr17:19801486-19801498 chr17:19801489-19801496 chr17:19801487-19801496 chr17:19801486-19801497
17	POLR2A	chr17:19800945-19801495	Hela-S3	cervix:	n/a	n/a
18	FOSL2	chr17:19801065-19801425	HepG2	liver:	n/a	chr17:19801184-19801193
19	GATA3	chr17:19801071-19801716	SK-N-SH	brain:	n/a	n/a
20	GATA3	chr17:19801186-19801699	T-47D	breast:	n/a	n/a
21	JUND	chr17:19801371-19801507	K562	blood:	n/a	chr17:19801486-19801498 chr17:19801489-19801496 chr17:19801487-19801496 chr17:19801486-19801497
22	POLR2A	chr17:19800387-19801559	MCF10A-Er-Src	breast:	n/a	n/a
23	POLR2A	chr17:19801099-19801505	GM12878	blood:	n/a	n/a
24	GATA3	chr17:19801207-19801594	MCF-7	breast:	n/a	n/a
25	FOS	chr17:19801326-19801665	MCF10A-Er-Src	breast:	n/a	chr17:19801486-19801498 chr17:19801489-19801496 chr17:19801487-19801496 chr17:19801486-19801497
26	FOSL2	chr17:19801264-19801727	MCF-7	breast:	n/a	chr17:19801486-19801498 chr17:19801489-19801496 chr17:19801487-19801496
27	POLR2A	chr17:19801067-19801467	Hela-S3	cervix:	n/a	n/a
28	JUND	chr17:19801188-19801757	SK-N-SH	brain:	n/a	chr17:19801486-19801498 chr17:19801489-19801496 chr17:19801487-19801496 chr17:19801486-19801497
29	POLR2A	chr17:19800639-19801494	U87	brain:	n/a	n/a
30	FOS	chr17:19801303-19801674	MCF10A-Er-Src	breast:	n/a	chr17:19801486-19801498 chr17:19801489-19801496 chr17:19801487-19801496 chr17:19801486-19801497
31	EP300	chr17:19801308-19801549	SK-N-SH_RA	brain:	n/a	chr17:19801487-19801496
32	TCF7L2	chr17:19801248-19801707	Hela-S3	cervix:	n/a	chr17:19801487-19801496
33	GATA3	chr17:19801121-19801746	A549	lung:	n/a	n/a
34	RAD21	chr17:19801322-19801660	Hela-S3	cervix:	n/a	n/a
35	JUND	chr17:19801359-19801619	HepG2	liver:	n/a	chr17:19801486-19801498 chr17:19801489-19801496 chr17:19801487-19801496 chr17:19801486-19801497
36	FOS	chr17:19801315-19801642	Hela-S3	cervix:	n/a	chr17:19801486-19801498 chr17:19801489-19801496 chr17:19801487-19801496 chr17:19801486-19801497
37	CEBPB	chr17:19801254-19801738	IMR90	lung:	n/a	n/a
38	STAT3	chr17:19801389-19801731	MCF10A-Er-Src	breast:	n/a	n/a
39	JUND	chr17:19801223-19801740	SK-N-SH	brain:	n/a	chr17:19801486-19801498 chr17:19801489-19801496 chr17:19801487-19801496 chr17:19801486-19801497
40	JUND	chr17:19801249-19801713	Hela-S3	cervix:	n/a	chr17:19801486-19801498 chr17:19801489-19801496 chr17:19801487-19801496 chr17:19801486-19801497
41	FOSL2	chr17:19801345-19801649	A549	lung:	n/a	chr17:19801486-19801498 chr17:19801489-19801496 chr17:19801487-19801496
42	MYC	chr17:19801325-19801661	MCF10A-Er-Src	breast:	n/a	n/a
43	POLR2A	chr17:19801130-19801501	H1-hESC	embryonic stem cell:	n/a	n/a
44	POLR2A	chr17:19800128-19801653	MCF10A-Er-Src	breast:	n/a	n/a
45	FOS	chr17:19801301-19801680	MCF10A-Er-Src	breast:	n/a	chr17:19801486-19801498 chr17:19801489-19801496 chr17:19801487-19801496 chr17:19801486-19801497
46	STAT3	chr17:19801399-19801668	MCF10A-Er-Src	breast:	n/a	n/a
47	GATA2	chr17:19801220-19801503	HUVEC	blood vessel:	n/a	n/a
48	FOS	chr17:19801380-19801651	HUVEC	blood vessel:	n/a	chr17:19801486-19801498 chr17:19801489-19801496 chr17:19801487-19801496 chr17:19801486-19801497
49	GTF2F1	chr17:19800323-19801545	Hela-S3	cervix:	n/a	n/a
50	FOSL2	chr17:19801238-19801713	A549	lung:	n/a	chr17:19801486-19801498 chr17:19801489-19801496 chr17:19801487-19801496

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:19769802..19772027-chr17:19799780..19804333,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000270091	TF binding region
ENSG00000083290	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs12450857	0.83[CEU][hapmap];1.00[CHB][hapmap]
rs12453720	0.82[CEU][hapmap];1.00[CHB][hapmap]
rs1638526	0.86[CEU][hapmap]
rs1638527	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs1638528	0.86[CEU][hapmap]
rs169413	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs17604987	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs17759609	1.00[CHB][hapmap]
rs203449	0.83[AMR][1000 genomes]
rs203454	0.82[AMR][1000 genomes]
rs203464	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs203467	0.91[CEU][hapmap];1.00[CHB][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs203475	0.91[CEU][hapmap];1.00[CHB][hapmap]
rs203476	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs203478	0.91[CEU][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs203480	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2108981	0.82[CEU][hapmap];1.00[CHB][hapmap]
rs3862151	1.00[CHB][hapmap]
rs403021	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs427033	0.87[CEU][hapmap];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4924802	1.00[CHB][hapmap]
rs4925055	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4925084	1.00[CHB][hapmap]
rs56005410	0.80[AFR][1000 genomes]
rs62066267	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6813	0.86[CEU][hapmap];0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs8079923	0.91[CEU][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs850622	0.91[CEU][hapmap];0.88[YRI][hapmap];0.81[AMR][1000 genomes];0.81[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	nsv1062853	chr17:19547912-20206601	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	nsv1063892	chr17:19564634-19808485	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
3	nsv482398	chr17:19673458-19808039	Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Enhancers Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv907868	chr17:19768924-20217122	Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Weak transcription Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
5	nsv518888	chr17:19789453-19804247	Genic enhancers Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv907869	chr17:19795774-19926836	Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4925054	AKAP10	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:19796400-19809800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr17:19798400-19804000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr17:19799200-19808400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr17:19799400-19803800	Weak transcription	Thymus	Thymus
5	chr17:19799400-19805000	Weak transcription	Fetal Intestine Large	intestine
6	chr17:19799600-19803800	Weak transcription	Primary T cells from cord blood	blood
7	chr17:19799800-19805200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
8	chr17:19799800-19806800	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr17:19799800-19807000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr17:19800000-19801600	Enhancers	Fetal Heart	heart
11	chr17:19800000-19802200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr17:19800200-19801600	Enhancers	Colon Smooth Muscle	Colon
13	chr17:19800200-19802000	Enhancers	A549	lung
14	chr17:19800200-19802200	Flanking Active TSS	Hela-S3	cervix
15	chr17:19800200-19802200	Enhancers	HSMMtube	muscle
16	chr17:19800200-19804000	Weak transcription	Primary T cells fromperipheralblood	blood
17	chr17:19800400-19801800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr17:19800400-19802000	Enhancers	NHEK	skin
19	chr17:19800400-19802200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr17:19800400-19802200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr17:19800400-19802400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr17:19800400-19802400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr17:19800600-19801600	Enhancers	Osteobl	bone
24	chr17:19800600-19802200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr17:19800600-19802200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr17:19800600-19802200	Enhancers	HSMM	muscle
27	chr17:19800600-19802200	Enhancers	NHDF-Ad	bronchial
28	chr17:19800600-19802800	Weak transcription	Primary neutrophils fromperipheralblood	blood
29	chr17:19800600-19802800	Weak transcription	Monocytes-CD14+_RO01746	blood
30	chr17:19800600-19803000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr17:19800600-19803000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
32	chr17:19800600-19807600	Weak transcription	Brain Angular Gyrus	brain
33	chr17:19800800-19802200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr17:19800800-19803000	Weak transcription	Fetal Muscle Trunk	muscle
35	chr17:19800800-19803000	Weak transcription	Skeletal Muscle Female	skeletal muscle
36	chr17:19800800-19803600	Weak transcription	Fetal Lung	lung
37	chr17:19800800-19803600	Weak transcription	Ovary	ovary
38	chr17:19800800-19803800	Weak transcription	Liver	Liver
39	chr17:19800800-19803800	Weak transcription	Skeletal Muscle Male	skeletal muscle
40	chr17:19801000-19801600	Enhancers	ES-I3 Cell Line	embryonic stem cell
41	chr17:19801000-19801600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr17:19801000-19803000	Weak transcription	Primary monocytes fromperipheralblood	blood
43	chr17:19801000-19803000	Weak transcription	Pancreas	Pancrea
44	chr17:19801000-19803800	Weak transcription	Spleen	Spleen
45	chr17:19801000-19808200	Weak transcription	Left Ventricle	heart
46	chr17:19801000-19808400	Weak transcription	Esophagus	oesophagus
47	chr17:19801200-19801600	Enhancers	Fetal Stomach	stomach
48	chr17:19801200-19802200	Enhancers	HUES64 Cell Line	embryonic stem cell
49	chr17:19801200-19802200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr17:19801200-19802200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell

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