Variant report

Variant	rs2405367
Chromosome Location	chr20:23622880-23622881
allele	A/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	RCOR1	chr20:23622864-23623663	IMR90	lung:	n/a	n/a
2	TCF12	chr20:23622773-23623557	SK-N-SH	brain:	n/a	n/a
3	RCOR1	chr20:23622818-23622931	HepG2	liver:	n/a	n/a
4	TCF12	chr20:23622761-23623663	SK-N-SH	brain:	n/a	n/a
5	FOSL2	chr20:23622841-23623593	SK-N-SH	brain:	n/a	chr20:23623300-23623310 chr20:23623301-23623309 chr20:23623299-23623311 chr20:23623302-23623313 chr20:23623300-23623310

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr20:23615698..23619686-chr20:23620113..23624171,4	MCF-7	breast:
2	chr20:23616967..23620200-chr20:23620235..23623406,7	MCF-7	breast:

Variant related genes	Relation type
CST3	TF binding region
ENSG00000101439	Chromatin interaction

Extended variants
information (count: 66 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs1010117	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1011226	0.85[CEU][hapmap];0.93[GIH][hapmap];0.86[JPT][hapmap];0.82[TSI][hapmap];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1064039	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1158167	0.80[CEU][hapmap]
rs12625716	0.85[CEU][hapmap];0.93[GIH][hapmap];0.86[JPT][hapmap];0.82[TSI][hapmap];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13037490	0.85[CEU][hapmap];0.86[JPT][hapmap];0.84[TSI][hapmap]
rs13038305	0.90[CEU][hapmap];0.86[JPT][hapmap];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13039536	0.85[JPT][hapmap];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13041070	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13043266	0.85[CEU][hapmap];0.86[JPT][hapmap]
rs13043610	0.85[CEU][hapmap];0.86[GIH][hapmap];0.86[JPT][hapmap];0.86[TSI][hapmap]
rs17751897	0.85[CEU][hapmap];0.93[GIH][hapmap];0.86[JPT][hapmap];0.82[TSI][hapmap]
rs2016161	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2254635	1.00[CEU][hapmap];0.82[CHB][hapmap];0.84[CHD][hapmap];0.98[GIH][hapmap];0.86[JPT][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2405392	0.81[CEU][hapmap]
rs2424582	1.00[CEU][hapmap];0.82[CHB][hapmap];0.84[CHD][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];0.96[TSI][hapmap];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28703706	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2897119	0.88[EUR][1000 genomes]
rs3088162	0.90[CEU][hapmap];0.86[JPT][hapmap];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34374560	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34746357	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34897231	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35488434	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35610040	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];0.88[ASN][1000 genomes]
rs35966482	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3761280	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3761281	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3787498	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]
rs3787499	0.95[CEU][hapmap];0.82[CHB][hapmap];0.84[CHD][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];0.90[TSI][hapmap];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3810575	0.81[CEU][hapmap];0.86[JPT][hapmap]
rs3827141	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];0.88[ASN][1000 genomes]
rs3827142	0.95[CEU][hapmap];0.82[CHB][hapmap];0.84[CHD][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];0.90[TSI][hapmap];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3827143	0.95[CEU][hapmap];0.82[CHB][hapmap];0.84[CHD][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];0.93[TSI][hapmap];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4346460	0.81[CEU][hapmap]
rs4815222	0.81[CEU][hapmap]
rs4815223	0.83[CEU][hapmap]
rs4815224	0.90[CEU][hapmap];0.91[GIH][hapmap];0.86[JPT][hapmap];0.90[TSI][hapmap]
rs5030707	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6036461	0.81[CEU][hapmap]
rs6036465	0.81[CEU][hapmap];0.88[GIH][hapmap];0.86[JPT][hapmap];0.82[TSI][hapmap]
rs6036474	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6036476	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6036478	0.85[CEU][hapmap];0.98[GIH][hapmap];0.86[JPT][hapmap];0.82[TSI][hapmap];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6048920	0.81[CEU][hapmap]
rs6048923	0.85[CEU][hapmap]
rs6048928	0.85[CEU][hapmap];0.86[GIH][hapmap];0.86[JPT][hapmap];0.86[TSI][hapmap]
rs6048929	0.81[CEU][hapmap];0.86[JPT][hapmap]
rs6048930	0.85[CEU][hapmap];0.86[JPT][hapmap]
rs6048952	0.85[CEU][hapmap];0.93[GIH][hapmap];0.86[JPT][hapmap];0.82[TSI][hapmap];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6048956	0.90[CEU][hapmap];0.86[JPT][hapmap];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6114201	0.85[CEU][hapmap];0.86[JPT][hapmap];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6114206	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6114208	0.90[CEU][hapmap];0.86[JPT][hapmap];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6114209	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6515375	0.86[JPT][hapmap];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs67567111	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs71334202	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73318135	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs734801	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8115417	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8115423	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8116859	0.85[CEU][hapmap];0.86[JPT][hapmap]
rs8121283	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8121405	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs911119	0.89[CEU][hapmap];0.86[JPT][hapmap];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2405367	CST3	Cis_1M	lymphoblastoid	RTeQTL
rs2405367	CST3	cis	parietal	SCAN
rs2405367	CST3	cis	cerebellum	SCAN
rs2405367	CST3	cis	multi-tissue	Pritchard

Chromatin state (count:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:23618600-23624800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr20:23618600-23626000	Weak transcription	Gastric	stomach
3	chr20:23618800-23623000	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr20:23618800-23623000	Weak transcription	NH-A	brain
5	chr20:23618800-23625200	Enhancers	Primary hematopoietic stem cells short term culture	blood
6	chr20:23618800-23626400	Weak transcription	Primary hematopoietic stem cells	blood
7	chr20:23618800-23628600	Enhancers	Primary monocytes fromperipheralblood	blood
8	chr20:23619400-23623000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr20:23620000-23623200	Enhancers	Spleen	Spleen
10	chr20:23620000-23625000	Enhancers	Fetal Thymus	thymus
11	chr20:23620200-23623600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr20:23620800-23623000	Enhancers	Thymus	Thymus
13	chr20:23620800-23623000	Weak transcription	HMEC	breast
14	chr20:23620800-23623000	Weak transcription	NHEK	skin
15	chr20:23620800-23623200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr20:23620800-23623400	Enhancers	ES-I3 Cell Line	embryonic stem cell
17	chr20:23620800-23624400	Enhancers	Fetal Muscle Leg	muscle
18	chr20:23621000-23623000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr20:23621200-23623400	Enhancers	Ovary	ovary
20	chr20:23621200-23623600	Enhancers	GM12878-XiMat	blood
21	chr20:23621200-23625200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr20:23621400-23623600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
23	chr20:23621400-23624800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr20:23621400-23625000	Enhancers	Adipose Nuclei	Adipose
25	chr20:23621600-23623000	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
26	chr20:23621600-23623600	Enhancers	Brain Hippocampus Middle	brain
27	chr20:23621600-23623800	Enhancers	HSMM	muscle
28	chr20:23621800-23623000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr20:23621800-23623600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
30	chr20:23621800-23623800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr20:23621800-23624600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr20:23622000-23623000	Enhancers	iPS-20b Cell Line	embryonic stem cell
33	chr20:23622000-23623000	Weak transcription	Liver	Liver
34	chr20:23622000-23623000	Weak transcription	Placenta	Placenta
35	chr20:23622000-23623600	Enhancers	Cortex derived primary cultured neurospheres	brain
36	chr20:23622000-23623600	Enhancers	HSMMtube	muscle
37	chr20:23622000-23623800	Enhancers	HUVEC	blood vessel
38	chr20:23622000-23624200	Weak transcription	Primary B cells from cord blood	blood
39	chr20:23622000-23625600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr20:23622200-23623800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr20:23622200-23623800	Enhancers	Muscle Satellite Cultured Cells	--
42	chr20:23622200-23624800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
43	chr20:23622200-23636600	Weak transcription	Pancreas	Pancrea
44	chr20:23622400-23623000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
45	chr20:23622400-23623000	Enhancers	HepG2	liver
46	chr20:23622400-23623200	Enhancers	HUES64 Cell Line	embryonic stem cell
47	chr20:23622400-23623200	Enhancers	Left Ventricle	heart
48	chr20:23622400-23623200	Enhancers	Lung	lung
49	chr20:23622400-23623400	Enhancers	Fetal Muscle Trunk	muscle
50	chr20:23622400-23623800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung

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