Variant report

Variant	rs73981807
Chromosome Location	chr17:19996230-19996231
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	KAP1	chr17:19995697-19996925	HEK293	kidney:	n/a	n/a
2	KAP1	chr17:19995607-19996877	U2OS	brain:	n/a	n/a
3	TCF7L2	chr17:19995744-19996580	PANC-1	pancreas:	n/a	chr17:19996060-19996076 chr17:19996061-19996075 chr17:19996064-19996073

No.	Distal block	Cell Line	Cell type
1	chr17:19894457..19896275-chr17:19994382..19996657,2	MCF-7	breast:
2	chr17:19994190..19996745-chr17:20058300..20060298,2	MCF-7	breast:
3	chr17:19995540..19998202-chr2:209032220..209035134,2	MCF-7	breast:

Variant related genes	Relation type
SPECC1	TF binding region
ENSG00000128487	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs12051550	0.88[EUR][1000 genomes]
rs13339684	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs16942325	0.87[EUR][1000 genomes]
rs16959946	0.89[EUR][1000 genomes]
rs16960660	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs16960678	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16964352	0.84[EUR][1000 genomes]
rs28550747	0.89[EUR][1000 genomes]
rs28567541	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs28622601	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs28644386	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3764436	0.94[EUR][1000 genomes]
rs5025290	0.89[EUR][1000 genomes]
rs56138907	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7210439	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7219770	0.91[ASN][1000 genomes]
rs7223910	0.91[ASN][1000 genomes]
rs7225605	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73981803	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73984564	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs73984568	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73984571	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73984573	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9889684	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9895177	0.89[EUR][1000 genomes]
rs9897161	0.89[EUR][1000 genomes]
rs9897168	0.89[EUR][1000 genomes]
rs9901357	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9901484	0.89[EUR][1000 genomes]
rs9902683	0.94[EUR][1000 genomes]
rs9908032	0.92[EUR][1000 genomes]
rs9908418	0.89[EUR][1000 genomes]
rs9909156	0.87[EUR][1000 genomes]
rs9911879	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9913018	0.89[EUR][1000 genomes]
rs9916729	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 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	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
10	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
rs73981807	USP32P3	cis	Nerve Tibial	GTEx
rs73981807	AKAP10	cis	Whole Blood	GTEx

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:19978800-20000000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr17:19990200-19998800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr17:19991200-19996800	Enhancers	Skeletal Muscle Male	skeletal muscle
4	chr17:19993000-19996800	Enhancers	Skeletal Muscle Female	skeletal muscle
5	chr17:19993200-19996600	Enhancers	Fetal Muscle Leg	muscle
6	chr17:19993400-20006400	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr17:19993600-19998600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
8	chr17:19993600-20000000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
9	chr17:19993600-20003600	Weak transcription	Primary neutrophils fromperipheralblood	blood
10	chr17:19993800-19996800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr17:19993800-19998600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr17:19993800-19998800	Weak transcription	Spleen	Spleen
13	chr17:19993800-20000600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr17:19993800-20001600	Weak transcription	Lung	lung
15	chr17:19993800-20006400	Weak transcription	Esophagus	oesophagus
16	chr17:19993800-20008800	Weak transcription	GM12878-XiMat	blood
17	chr17:19994000-19996800	Strong transcription	Primary monocytes fromperipheralblood	blood
18	chr17:19994000-19997800	Strong transcription	Monocytes-CD14+_RO01746	blood
19	chr17:19994400-19996800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr17:19994600-19996400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr17:19994600-19996800	Enhancers	H9 Cell Line	embryonic stem cell
22	chr17:19994600-19997000	Enhancers	HUES6 Cell Line	embryonic stem cell
23	chr17:19994600-19997000	Enhancers	iPS-18 Cell Line	embryonic stem cell
24	chr17:19994600-19997000	Enhancers	iPS-20b Cell Line	embryonic stem cell
25	chr17:19994600-19997000	Enhancers	Brain Cingulate Gyrus	brain
26	chr17:19994600-19997200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr17:19994600-19997200	Enhancers	Brain Anterior Caudate	brain
28	chr17:19994600-19998400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
29	chr17:19994600-19998600	Enhancers	Brain Hippocampus Middle	brain
30	chr17:19994800-19996800	Enhancers	H1 Cell Line	embryonic stem cell
31	chr17:19994800-19996800	Enhancers	iPS-15b Cell Line	embryonic stem cell
32	chr17:19994800-19997200	Enhancers	HUES64 Cell Line	embryonic stem cell
33	chr17:19995000-19996600	Enhancers	A549	lung
34	chr17:19995000-19997000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
35	chr17:19995000-20000000	Weak transcription	Right Ventricle	heart
36	chr17:19995000-20001200	Weak transcription	Primary hematopoietic stem cells	blood
37	chr17:19995200-19996600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
38	chr17:19995200-19996800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
39	chr17:19995200-19996800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr17:19995200-19998200	Weak transcription	Duodenum Smooth Muscle	Duodenum
41	chr17:19995200-19998800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr17:19995400-19996600	Enhancers	Aorta	Aorta
43	chr17:19995400-19998400	Enhancers	Brain Angular Gyrus	brain
44	chr17:19995400-19998600	Enhancers	Adipose Nuclei	Adipose
45	chr17:19995600-19996800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr17:19995600-19996800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr17:19995600-19996800	Enhancers	Brain Inferior Temporal Lobe	brain
48	chr17:19995600-19997600	Enhancers	Ovary	ovary
49	chr17:19995600-19998400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr17:19995800-19997000	Enhancers	Left Ventricle	heart

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