Variant report

Variant	rs7215803
Chromosome Location	chr17:19998377-19998378
allele	C/T
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	FOS	chr17:19998179-19998443	MCF10A-Er-Src	breast:	n/a	chr17:19998292-19998304 chr17:19998294-19998302 chr17:19998293-19998304
2	RAD21	chr17:19998159-19999582	SK-N-SH	brain:	n/a	chr17:19998781-19998795 chr17:19998728-19998740
3	KAP1	chr17:19998316-19999070	HEK293	kidney:	n/a	n/a
4	MXI1	chr17:19998190-19999434	SK-N-SH	brain:	n/a	chr17:19998462-19998477
5	CTCF	chr17:19998181-19999885	A549	lung:	n/a	n/a
6	FOS	chr17:19998156-19998444	MCF10A-Er-Src	breast:	n/a	chr17:19998292-19998304 chr17:19998294-19998302 chr17:19998293-19998304

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:19912080..19913024-chr17:19997997..19998740,2	K562	blood:

Variant related genes	Relation type
SPECC1	TF binding region
ENSG00000128487	Chromatin interaction
ENSG00000261033	Chromatin interaction

Extended variants
information (count: 93 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:84)

rs_ID	r²[population]
rs10083830	0.89[AMR][1000 genomes]
rs10083840	0.91[AMR][1000 genomes]
rs11204422	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.96[MKK][hapmap];0.98[TSI][hapmap];0.85[YRI][hapmap];0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11654025	0.85[CHD][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs11867585	0.90[JPT][hapmap]
rs11869931	1.00[ASN][1000 genomes]
rs11870381	0.86[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs11870673	0.85[ASN][1000 genomes]
rs12451216	0.92[ASN][1000 genomes]
rs12451841	0.93[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.95[TSI][hapmap];0.95[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12453332	0.97[ASN][1000 genomes]
rs12942179	0.80[CEU][hapmap];0.90[JPT][hapmap];0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12947713	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12949710	1.00[ASN][1000 genomes]
rs1468953	1.00[ASN][1000 genomes]
rs1638526	0.90[JPT][hapmap]
rs17685923	1.00[ASN][1000 genomes]
rs17686798	0.86[CHB][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.88[ASN][1000 genomes]
rs17759083	0.91[AMR][1000 genomes]
rs17759609	0.87[MEX][hapmap]
rs17759959	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs1812934	0.82[MEX][hapmap]
rs2013441	0.87[MEX][hapmap]
rs2034110	1.00[JPT][hapmap]
rs2072337	0.90[JPT][hapmap]
rs2107566	0.82[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	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34756775	1.00[ASN][1000 genomes]
rs35041742	0.85[ASN][1000 genomes]
rs35124809	1.00[ASN][1000 genomes]
rs35156798	0.97[ASN][1000 genomes]
rs35191778	1.00[ASN][1000 genomes]
rs35244101	1.00[ASN][1000 genomes]
rs35493088	1.00[ASN][1000 genomes]
rs35770292	0.97[ASN][1000 genomes]
rs36051592	0.87[ASN][1000 genomes]
rs3850783	0.83[MEX][hapmap]
rs4141185	0.90[JPT][hapmap]
rs4341795	1.00[ASN][1000 genomes]
rs4346259	1.00[ASN][1000 genomes]
rs4350625	1.00[ASN][1000 genomes]
rs4471741	1.00[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];0.92[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];0.91[MEX][hapmap];1.00[ASN][1000 genomes]
rs4925076	1.00[ASN][1000 genomes]
rs4925078	1.00[ASN][1000 genomes]
rs4925082	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]
rs4925084	0.84[CEU][hapmap]
rs4925088	0.85[CHD][hapmap];0.82[JPT][hapmap];0.87[MEX][hapmap];0.86[TSI][hapmap];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs57146223	0.80[ASN][1000 genomes]
rs62067488	1.00[ASN][1000 genomes]
rs6587207	1.00[JPT][hapmap]
rs7207459	1.00[JPT][hapmap]
rs7209653	0.90[JPT][hapmap]
rs7224875	1.00[JPT][hapmap]
rs7225249	0.90[JPT][hapmap]
rs7503407	1.00[ASN][1000 genomes]
rs8066705	0.88[ASN][1000 genomes]
rs8068484	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs8074791	0.88[ASN][1000 genomes]
rs8075343	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs8080190	1.00[JPT][hapmap]
rs8081817	1.00[ASN][1000 genomes]
rs888424	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];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs972966	0.88[ASN][1000 genomes]
rs9897328	0.83[MEX][hapmap]
rs9897653	0.90[JPT][hapmap]
rs9901125	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9901294	0.90[JPT][hapmap]
rs9904928	0.82[MEX][hapmap]
rs9915039	1.00[JPT][hapmap]
rs9944451	0.90[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7215803	CYTSB	cis	cerebellum	SCAN
rs7215803	AKAP10	cis	lymphoblastoid	seeQTL

Chromatin state (count:64 , 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	chr17:19993400-20006400	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr17:19993600-19998600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
5	chr17:19993600-20000000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
6	chr17:19993600-20003600	Weak transcription	Primary neutrophils fromperipheralblood	blood
7	chr17:19993800-19998600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr17:19993800-19998800	Weak transcription	Spleen	Spleen
9	chr17:19993800-20000600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr17:19993800-20001600	Weak transcription	Lung	lung
11	chr17:19993800-20006400	Weak transcription	Esophagus	oesophagus
12	chr17:19993800-20008800	Weak transcription	GM12878-XiMat	blood
13	chr17:19994600-19998400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
14	chr17:19994600-19998600	Enhancers	Brain Hippocampus Middle	brain
15	chr17:19995000-20000000	Weak transcription	Right Ventricle	heart
16	chr17:19995000-20001200	Weak transcription	Primary hematopoietic stem cells	blood
17	chr17:19995200-19998800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr17:19995400-19998400	Enhancers	Brain Angular Gyrus	brain
19	chr17:19995400-19998600	Enhancers	Adipose Nuclei	Adipose
20	chr17:19995600-19998400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr17:19995800-19998800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr17:19996600-20000800	Weak transcription	Aorta	Aorta
23	chr17:19996800-19998400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
24	chr17:19996800-19998400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
25	chr17:19996800-19998800	Weak transcription	H1 Cell Line	embryonic stem cell
26	chr17:19996800-19998800	Weak transcription	H9 Cell Line	embryonic stem cell
27	chr17:19996800-19998800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr17:19996800-19999600	Weak transcription	Primary monocytes fromperipheralblood	blood
29	chr17:19997000-19998400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
30	chr17:19997000-19998400	Weak transcription	HUES48 Cell Line	embryonic stem cell
31	chr17:19997000-19998400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
32	chr17:19997000-19998600	Weak transcription	HUES6 Cell Line	embryonic stem cell
33	chr17:19997000-19998800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
34	chr17:19997000-19998800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr17:19997000-19998800	Weak transcription	Left Ventricle	heart
36	chr17:19997200-19998400	Weak transcription	HUES64 Cell Line	embryonic stem cell
37	chr17:19997400-19998400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr17:19997400-19998600	Weak transcription	Right Atrium	heart
39	chr17:19997600-19998400	Enhancers	Brain Anterior Caudate	brain
40	chr17:19997600-19998400	Enhancers	Skeletal Muscle Female	skeletal muscle
41	chr17:19997600-19998800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
42	chr17:19997600-19998800	Weak transcription	Ovary	ovary
43	chr17:19997600-19999600	Enhancers	Fetal Muscle Leg	muscle
44	chr17:19997800-19998400	Enhancers	A549	lung
45	chr17:19997800-19999000	Enhancers	NHLF	lung
46	chr17:19997800-19999200	Enhancers	Brain Germinal Matrix	brain
47	chr17:19997800-19999200	Weak transcription	Monocytes-CD14+_RO01746	blood
48	chr17:19998200-19998400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr17:19998200-19998400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr17:19998200-19998400	Active TSS	Brain Cingulate Gyrus	brain

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