Variant report

Variant	rs4925082
Chromosome Location	chr17:19994673-19994674
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:19894457..19896275-chr17:19994382..19996657,2	MCF-7	breast:
2	chr17:19969588..19972096-chr17:19993265..19995045,2	K562	blood:
3	chr17:19980057..19981963-chr17:19993152..19995446,2	K562	blood:
4	chr17:19991773..19994998-chr2:209032034..209035004,3	K562	blood:
5	chr17:19993292..19995156-chr17:20055465..20057406,2	MCF-7	breast:
6	chr17:19994190..19996745-chr17:20058300..20060298,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000128487	Chromatin interaction

Extended variants
information (count: 92 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:81)

rs_ID	r²[population]
rs10083830	0.92[AMR][1000 genomes]
rs10083840	0.90[AMR][1000 genomes]
rs11204422	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.96[MKK][hapmap];0.98[TSI][hapmap];0.90[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11867585	0.90[JPT][hapmap]
rs11869931	0.98[ASN][1000 genomes]
rs11870381	0.86[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs11870673	0.83[ASN][1000 genomes]
rs12451216	0.90[ASN][1000 genomes]
rs12451841	0.87[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.95[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12453332	0.95[ASN][1000 genomes]
rs12942179	0.80[CEU][hapmap];0.90[JPT][hapmap];0.81[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12947713	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs12949710	0.98[ASN][1000 genomes]
rs1468953	0.98[ASN][1000 genomes]
rs1638526	0.90[JPT][hapmap]
rs17685923	0.98[ASN][1000 genomes]
rs17686798	0.86[CHB][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.87[ASN][1000 genomes]
rs17759083	0.90[AMR][1000 genomes]
rs17759609	0.84[MEX][hapmap]
rs17759959	1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs1812934	0.83[MEX][hapmap]
rs2013441	0.88[MEX][hapmap]
rs2072337	0.90[JPT][hapmap]
rs2107566	0.83[MEX][hapmap]
rs2189710	0.83[MEX][hapmap]
rs2526475	0.83[MEX][hapmap]
rs2526480	0.83[MEX][hapmap]
rs2703774	0.83[MEX][hapmap]
rs2703804	0.83[MEX][hapmap]
rs2703815	0.83[MEX][hapmap]
rs2703817	0.83[MEX][hapmap]
rs28424266	0.90[JPT][hapmap]
rs34089239	0.83[MEX][hapmap]
rs34370440	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34756775	0.98[ASN][1000 genomes]
rs35041742	0.84[ASN][1000 genomes]
rs35124809	0.98[ASN][1000 genomes]
rs35156798	0.95[ASN][1000 genomes]
rs35191778	0.98[ASN][1000 genomes]
rs35244101	0.98[ASN][1000 genomes]
rs35493088	0.98[ASN][1000 genomes]
rs35770292	0.95[ASN][1000 genomes]
rs36051592	0.85[ASN][1000 genomes]
rs3850783	0.83[MEX][hapmap]
rs4141185	0.90[JPT][hapmap]
rs4341795	0.98[ASN][1000 genomes]
rs4346259	0.98[ASN][1000 genomes]
rs4350625	0.98[ASN][1000 genomes]
rs4471741	0.98[ASN][1000 genomes]
rs4570919	0.90[JPT][hapmap]
rs4588033	0.83[MEX][hapmap]
rs4924808	0.86[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.90[ASN][1000 genomes]
rs4924810	0.83[MEX][hapmap]
rs4925075	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.98[ASN][1000 genomes]
rs4925076	0.98[ASN][1000 genomes]
rs4925078	0.98[ASN][1000 genomes]
rs4925084	0.84[CEU][hapmap]
rs4925088	0.85[CHD][hapmap];0.81[GIH][hapmap];0.82[JPT][hapmap];0.88[MEX][hapmap];0.86[TSI][hapmap];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62067488	0.98[ASN][1000 genomes]
rs6587207	1.00[JPT][hapmap]
rs7207459	1.00[JPT][hapmap]
rs7209653	0.90[JPT][hapmap]
rs7215803	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7224875	1.00[JPT][hapmap]
rs7225249	0.90[JPT][hapmap]
rs7503407	0.98[ASN][1000 genomes]
rs8066705	0.87[ASN][1000 genomes]
rs8068484	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs8074791	0.87[ASN][1000 genomes]
rs8075343	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs8080190	1.00[JPT][hapmap]
rs8081817	0.98[ASN][1000 genomes]
rs888424	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs972966	0.87[ASN][1000 genomes]
rs9897328	0.83[MEX][hapmap]
rs9897653	0.90[JPT][hapmap]
rs9901125	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9901294	0.90[JPT][hapmap]
rs9904928	0.83[MEX][hapmap]
rs9915039	1.00[JPT][hapmap]
rs9944451	0.90[JPT][hapmap];0.81[YRI][hapmap]

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	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	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
11	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
rs4925082	CYTSB	cis	cerebellum	SCAN
rs4925082	AKAP10	cis	lymphoblastoid	seeQTL

Chromatin state (count:61 , 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	chr17:19990000-19995600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr17:19990200-19994800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr17:19990200-19995000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr17:19990200-19998800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr17:19990600-19995000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr17:19991200-19994800	Weak transcription	Brain Angular Gyrus	brain
8	chr17:19991200-19995000	Weak transcription	A549	lung
9	chr17:19991200-19996800	Enhancers	Skeletal Muscle Male	skeletal muscle
10	chr17:19992600-19995400	Weak transcription	Aorta	Aorta
11	chr17:19993000-19996800	Enhancers	Skeletal Muscle Female	skeletal muscle
12	chr17:19993200-19994800	Enhancers	Adipose Nuclei	Adipose
13	chr17:19993200-19996600	Enhancers	Fetal Muscle Leg	muscle
14	chr17:19993400-20006400	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr17:19993600-19996000	Enhancers	NHDF-Ad	bronchial
16	chr17:19993600-19998600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr17:19993600-20000000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
18	chr17:19993600-20003600	Weak transcription	Primary neutrophils fromperipheralblood	blood
19	chr17:19993800-19995200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr17:19993800-19995800	Weak transcription	Left Ventricle	heart
21	chr17:19993800-19996800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr17:19993800-19998600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr17:19993800-19998800	Weak transcription	Spleen	Spleen
24	chr17:19993800-20000600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr17:19993800-20001600	Weak transcription	Lung	lung
26	chr17:19993800-20006400	Weak transcription	Esophagus	oesophagus
27	chr17:19993800-20008800	Weak transcription	GM12878-XiMat	blood
28	chr17:19994000-19995000	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
29	chr17:19994000-19995000	Enhancers	Right Ventricle	heart
30	chr17:19994000-19995200	Enhancers	Ovary	ovary
31	chr17:19994000-19996200	Enhancers	NH-A	brain
32	chr17:19994000-19996800	Strong transcription	Primary monocytes fromperipheralblood	blood
33	chr17:19994000-19997800	Strong transcription	Monocytes-CD14+_RO01746	blood
34	chr17:19994400-19996000	Enhancers	Fetal Muscle Trunk	muscle
35	chr17:19994400-19996800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
36	chr17:19994600-19994800	Enhancers	Primary hematopoietic stem cells	blood
37	chr17:19994600-19994800	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr17:19994600-19994800	Enhancers	Rectal Mucosa Donor 31	rectum
39	chr17:19994600-19995000	Enhancers	Right Atrium	heart
40	chr17:19994600-19995200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr17:19994600-19995200	Enhancers	Brain Inferior Temporal Lobe	brain
42	chr17:19994600-19995200	Enhancers	Brain Substantia Nigra	brain
43	chr17:19994600-19995200	Bivalent Enhancer	NHLF	lung
44	chr17:19994600-19995400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr17:19994600-19995400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr17:19994600-19995400	Flanking Active TSS	Osteobl	bone
47	chr17:19994600-19995600	Enhancers	HUES48 Cell Line	embryonic stem cell
48	chr17:19994600-19995600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr17:19994600-19995600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr17:19994600-19995600	Enhancers	Fetal Stomach	stomach

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