Variant report

Variant	rs3787498
Chromosome Location	chr20:23616781-23616782
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	POLR2A	chr20:23616697-23617084	K562	blood:	n/a	n/a
2	POLR2A	chr20:23614494-23618787	HepG2	liver:	n/a	n/a
3	POLR2A	chr20:23611829-23619325	HepG2	liver:	n/a	n/a
4	POLR2A	chr20:23616731-23617500	A549	lung:	n/a	n/a
5	POLR2A	chr20:23615259-23617766	HepG2	liver:	n/a	n/a
6	POLR2A	chr20:23616779-23617553	HepG2	liver:	n/a	n/a
7	HEY1	chr20:23615393-23617806	HepG2	liver:	n/a	n/a
8	POLR2A	chr20:23614496-23617566	HepG2	liver:	n/a	n/a
9	POLR2A	chr20:23611753-23618814	HepG2	liver:	n/a	n/a
10	POLR2A	chr20:23615326-23618779	MCF10A-Er-Src	breast:	n/a	n/a
11	POLR2A	chr20:23616635-23617010	K562	blood:	n/a	n/a
12	HEY1	chr20:23616708-23618722	HepG2	liver:	n/a	chr20:23617977-23617992 chr20:23618207-23618222 chr20:23617985-23618000

No.	Distal block	Cell Line	Cell type
1	chr20:23604645..23607070-chr20:23613987..23616956,2	K562	blood:
2	chr20:23400310..23402508-chr20:23615661..23618868,3	MCF-7	breast:
3	chr20:23608610..23615599-chr20:23616056..23619619,19	MCF-7	breast:
4	chr20:23615491..23618366-chr20:23625789..23627708,2	MCF-7	breast:
5	chr20:23342009..23344759-chr20:23616093..23619702,3	MCF-7	breast:
6	chr20:23615462..23617688-chr20:23624542..23627030,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000270001	TF binding region
ENSG00000125812	Chromatin interaction
ENSG00000270001	Chromatin interaction
ENSG00000125814	Chromatin interaction

Extended variants
information (count: 105 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:103)

rs_ID	r²[population]
rs1010117	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1011226	0.90[CEU][hapmap];0.82[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.91[TSI][hapmap];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1064039	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1158167	0.85[CEU][hapmap];0.88[JPT][hapmap];0.84[TSI][hapmap];0.80[EUR][1000 genomes]
rs12624424	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12625182	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12625716	0.90[CEU][hapmap];0.82[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.91[TSI][hapmap];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13037490	0.90[CEU][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.93[TSI][hapmap];0.84[EUR][1000 genomes]
rs13038305	0.95[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13038337	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13038990	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13039536	1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13040663	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13041070	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13043266	0.90[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes]
rs13043610	0.90[CEU][hapmap];0.82[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.97[TSI][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1555355	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17751897	0.90[CEU][hapmap];0.82[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.91[TSI][hapmap];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2016161	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2067488	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2208289	0.80[EUR][1000 genomes]
rs2254635	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2405367	0.95[CEU][hapmap];0.82[CHB][hapmap];0.84[CHD][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];0.90[TSI][hapmap];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2405392	0.86[CEU][hapmap];0.88[JPT][hapmap]
rs2424582	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28703706	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2897119	0.81[EUR][1000 genomes]
rs3004139	0.80[EUR][1000 genomes]
rs3004145	0.80[EUR][1000 genomes]
rs3088162	0.95[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34374560	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34746357	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34792920	0.83[EUR][1000 genomes]
rs34897231	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34911568	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs35488434	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35573837	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35610040	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35782710	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs35966482	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3761280	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3761281	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3787499	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3810575	0.86[CEU][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap];0.80[EUR][1000 genomes]
rs3827141	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3827142	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3827143	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4346460	0.86[CEU][hapmap];0.88[JPT][hapmap];0.81[TSI][hapmap]
rs4815222	0.86[CEU][hapmap];0.88[JPT][hapmap];0.84[TSI][hapmap];0.80[EUR][1000 genomes]
rs4815223	0.89[CEU][hapmap];0.80[EUR][1000 genomes]
rs4815224	0.95[CEU][hapmap];0.82[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs5030707	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55897275	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs56371840	0.84[EUR][1000 genomes]
rs56388902	0.84[EUR][1000 genomes]
rs57549987	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs59059917	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6036461	0.86[CEU][hapmap];0.88[JPT][hapmap];0.84[TSI][hapmap];0.80[EUR][1000 genomes]
rs6036463	0.80[EUR][1000 genomes]
rs6036465	0.86[CEU][hapmap];0.82[CHB][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.91[TSI][hapmap];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6036469	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6036470	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6036471	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6036474	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6036476	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6036478	0.90[CEU][hapmap];0.89[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6048920	0.86[CEU][hapmap];0.88[JPT][hapmap];0.84[TSI][hapmap];0.80[EUR][1000 genomes]
rs6048922	0.80[EUR][1000 genomes]
rs6048923	0.90[CEU][hapmap];0.88[JPT][hapmap];0.84[EUR][1000 genomes]
rs6048924	0.80[EUR][1000 genomes]
rs6048928	0.90[CEU][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.97[TSI][hapmap];0.86[EUR][1000 genomes]
rs6048929	0.86[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6048930	0.90[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap]
rs6048933	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6048936	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6048941	0.82[EUR][1000 genomes]
rs6048945	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6048946	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6048949	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6048950	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6048952	0.90[CEU][hapmap];0.82[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.91[TSI][hapmap];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6048956	0.95[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61035931	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6114201	0.90[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6114206	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6114208	0.95[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6114209	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6515375	0.83[CEU][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs67567111	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67997662	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs71334202	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7265178	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7270413	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs73318135	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs734801	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8114619	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8115417	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8115423	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8116859	0.90[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8121147	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8121283	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8121405	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs911119	0.94[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv491876	chr20:23436633-24031374	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv964381	chr20:23614805-23621846	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs3787498	CST3	cis	cerebellum	SCAN
rs3787498	CST3	Cis_1M	lymphoblastoid	RTeQTL
rs3787498	CST3	cis	lymphoblastoid	seeQTL
rs3787498	CST3	cis	parietal	SCAN

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:23600600-23617000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr20:23602000-23616800	Weak transcription	H1 Cell Line	embryonic stem cell
3	chr20:23604000-23616800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr20:23606600-23617000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr20:23609800-23616800	Weak transcription	Primary hematopoietic stem cells	blood
6	chr20:23610200-23616800	Weak transcription	HUES6 Cell Line	embryonic stem cell
7	chr20:23610200-23617000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr20:23610200-23617000	Weak transcription	K562	blood
9	chr20:23610400-23616800	Weak transcription	HUES64 Cell Line	embryonic stem cell
10	chr20:23610400-23616800	Weak transcription	NH-A	brain
11	chr20:23610400-23618200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
12	chr20:23610600-23616800	Weak transcription	Hela-S3	cervix
13	chr20:23610800-23616800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
14	chr20:23610800-23617400	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr20:23612000-23617000	Genic enhancers	Fetal Muscle Trunk	muscle
16	chr20:23612600-23617200	Genic enhancers	Fetal Muscle Leg	muscle
17	chr20:23612800-23617200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr20:23613000-23616800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr20:23613800-23617200	Weak transcription	Pancreatic Islets	Pancreatic Islet
20	chr20:23614600-23617200	Genic enhancers	Gastric	stomach
21	chr20:23614600-23617400	Transcr. at gene 5' and 3'	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr20:23614800-23617200	Genic enhancers	Lung	lung
23	chr20:23614800-23617200	Genic enhancers	Spleen	Spleen
24	chr20:23614800-23617400	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr20:23614800-23617400	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr20:23615000-23616800	Weak transcription	Thymus	Thymus
27	chr20:23615000-23616800	Weak transcription	A549	lung
28	chr20:23615000-23617000	Transcr. at gene 5' and 3'	Skeletal Muscle Male	skeletal muscle
29	chr20:23615000-23618000	Transcr. at gene 5' and 3'	Cortex derived primary cultured neurospheres	brain
30	chr20:23615200-23617000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr20:23615200-23617000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
32	chr20:23615200-23617000	Transcr. at gene 5' and 3'	HepG2	liver
33	chr20:23615400-23616800	Enhancers	Brain Germinal Matrix	brain
34	chr20:23615400-23617200	Enhancers	Placenta	Placenta
35	chr20:23615600-23617000	Genic enhancers	Fetal Lung	lung
36	chr20:23615600-23617200	Enhancers	HUVEC	blood vessel
37	chr20:23615600-23617400	Transcr. at gene 5' and 3'	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr20:23615600-23617400	Transcr. at gene 5' and 3'	Primary monocytes fromperipheralblood	blood
39	chr20:23615800-23616800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr20:23615800-23616800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr20:23615800-23616800	Enhancers	Esophagus	oesophagus
42	chr20:23615800-23616800	Enhancers	HMEC	breast
43	chr20:23615800-23616800	Enhancers	NHDF-Ad	bronchial
44	chr20:23615800-23617200	Genic enhancers	Aorta	Aorta
45	chr20:23615800-23617200	Enhancers	Fetal Brain Male	brain
46	chr20:23615800-23617800	Flanking Active TSS	Adipose Nuclei	Adipose
47	chr20:23615800-23618000	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
48	chr20:23616000-23616800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr20:23616000-23616800	Enhancers	Liver	Liver
50	chr20:23616000-23616800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain

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