Variant report

Variant	rs56138907
Chromosome Location	chr17:19989045-19989046
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:19880813..19883681-chr17:19988880..19990706,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000108599	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs12051550	0.88[EUR][1000 genomes]
rs13339684	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs16942325	0.87[EUR][1000 genomes]
rs16959946	0.89[EUR][1000 genomes]
rs16960660	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16960678	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16964352	0.84[EUR][1000 genomes]
rs28550747	0.89[EUR][1000 genomes]
rs28567541	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28622601	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28644386	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3764436	0.89[EUR][1000 genomes]
rs5025290	0.89[EUR][1000 genomes]
rs7210439	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7219770	0.91[ASN][1000 genomes]
rs7223910	0.91[ASN][1000 genomes]
rs7225605	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73981803	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73981807	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73984564	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs73984568	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73984571	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73984573	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9889684	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9897161	0.89[EUR][1000 genomes]
rs9897168	0.89[EUR][1000 genomes]
rs9901357	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9901484	0.89[EUR][1000 genomes]
rs9902683	0.89[EUR][1000 genomes]
rs9908032	0.87[EUR][1000 genomes]
rs9909156	0.87[EUR][1000 genomes]
rs9911879	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9913018	0.89[EUR][1000 genomes]
rs9916729	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 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	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
3	nsv833394	chr17:19827714-19999577	Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
4	nsv1060337	chr17:19828636-20204872	Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
5	nsv543257	chr17:19828636-20204872	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
6	nsv907870	chr17:19871922-20001612	Enhancers Flanking Active TSS Strong transcription Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
7	nsv907871	chr17:19927699-20088492	Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
8	nsv482438	chr17:19934376-20089005	Enhancers Weak transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
9	nsv907872	chr17:19945841-19996140	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
10	nsv1056224	chr17:19946604-19993026	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
11	nsv543258	chr17:19946604-19993026	Weak transcription Bivalent Enhancer Enhancers Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
12	nsv833395	chr17:19969959-20124084	Genic enhancers Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
13	esv2762522	chr17:19976462-19996429	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs56138907	AKAP10	cis	Whole Blood	GTEx
rs56138907	USP32P3	cis	Nerve Tibial	GTEx

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:19976200-19989400	Weak transcription	Lung	lung
2	chr17:19977600-19989600	Weak transcription	K562	blood
3	chr17:19978800-20000000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr17:19980600-19994600	Weak transcription	Primary hematopoietic stem cells	blood
5	chr17:19980800-19990000	Weak transcription	A549	lung
6	chr17:19981200-19993000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
7	chr17:19982600-19993000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr17:19983200-19993400	Weak transcription	Spleen	Spleen
9	chr17:19985000-19989400	Weak transcription	Right Ventricle	heart
10	chr17:19985600-19993000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
11	chr17:19986200-19993000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr17:19986400-19990600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr17:19986400-19991400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr17:19986800-19989200	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr17:19987000-19994600	Weak transcription	HUES48 Cell Line	embryonic stem cell
16	chr17:19987800-19990200	Enhancers	NHDF-Ad	bronchial
17	chr17:19988000-19989200	Enhancers	NHLF	lung
18	chr17:19988000-19990200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr17:19988000-19990200	Enhancers	Ovary	ovary
20	chr17:19988000-19991200	Enhancers	Brain Angular Gyrus	brain
21	chr17:19988200-19989600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
22	chr17:19988200-19989600	Enhancers	Breast Myoepithelial Primary Cells	Breast
23	chr17:19988200-19990000	Enhancers	Skeletal Muscle Female	skeletal muscle
24	chr17:19988200-19990200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr17:19988200-19990200	Enhancers	Brain Anterior Caudate	brain
26	chr17:19988200-19990200	Enhancers	Brain Hippocampus Middle	brain
27	chr17:19988200-19990200	Enhancers	Brain Substantia Nigra	brain
28	chr17:19988200-19990200	Enhancers	Left Ventricle	heart
29	chr17:19988200-19990200	Enhancers	Skeletal Muscle Male	skeletal muscle
30	chr17:19988200-19990200	Enhancers	NH-A	brain
31	chr17:19988200-19990400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr17:19988200-19990400	Enhancers	Brain Inferior Temporal Lobe	brain
33	chr17:19988200-19990400	Enhancers	Fetal Muscle Trunk	muscle
34	chr17:19988200-19990600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr17:19988200-19991000	Enhancers	HSMMtube	muscle
36	chr17:19988200-19991200	Enhancers	Adipose Nuclei	Adipose
37	chr17:19988200-19991200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
38	chr17:19988400-19989200	Enhancers	Osteobl	bone
39	chr17:19988400-19989400	Enhancers	Brain Germinal Matrix	brain
40	chr17:19988400-19989600	Enhancers	HSMM	muscle
41	chr17:19988400-19989800	Genic enhancers	Monocytes-CD14+_RO01746	blood
42	chr17:19988400-19990200	Enhancers	Esophagus	oesophagus
43	chr17:19988400-19990400	Enhancers	Cortex derived primary cultured neurospheres	brain
44	chr17:19988600-19989200	Weak transcription	Aorta	Aorta
45	chr17:19988600-19989400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr17:19988600-19990000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr17:19988600-19990200	Strong transcription	Primary monocytes fromperipheralblood	blood
48	chr17:19988600-19993200	Weak transcription	GM12878-XiMat	blood
49	chr17:19988600-19994600	Weak transcription	HUES6 Cell Line	embryonic stem cell
50	chr17:19988800-19989200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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