Variant report

Variant	rs2424582
Chromosome Location	chr20:23622550-23622551
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	CTCF	chr20:23622460-23622610	HPAF	blood vessel:	n/a	n/a
2	CTCF	chr20:23622500-23622650	AG09319	gingival:	n/a	n/a
3	CTCF	chr20:23622500-23622650	RPTEC	kidney:	n/a	n/a
4	CTCF	chr20:23622440-23622590	GM12873	blood:	n/a	n/a
5	CTCF	chr20:23622480-23622630	AG04449	skin:	n/a	n/a
6	EP300	chr20:23621918-23622561	HepG2	liver:	n/a	chr20:23621979-23621993 chr20:23621940-23621956
7	CTCF	chr20:23622500-23622650	NHLF	lung:	n/a	n/a
8	CTCF	chr20:23622480-23622630	HPAF	blood vessel:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr20:23615698..23619686-chr20:23620113..23624171,4	MCF-7	breast:
2	chr20:23616967..23620200-chr20:23620235..23623406,7	MCF-7	breast:
3	chr20:23617967..23620245-chr20:23621003..23622581,2	K562	blood:

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

Extended variants
information (count: 93 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:92)

rs_ID	r²[population]
rs1010117	0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1011226	0.85[CEU][hapmap];0.82[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1064039	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1158167	0.80[CEU][hapmap];0.88[JPT][hapmap];0.91[MEX][hapmap]
rs12624424	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12625182	0.83[ASN][1000 genomes]
rs12625716	0.85[CEU][hapmap];0.82[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13037490	0.85[CEU][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap]
rs13038305	0.90[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13038337	0.82[ASN][1000 genomes]
rs13038990	0.82[ASN][1000 genomes]
rs13039536	1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13041070	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13043266	0.85[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap]
rs13043610	0.85[CEU][hapmap];0.82[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap]
rs1555355	0.82[ASN][1000 genomes]
rs17751897	0.85[CEU][hapmap];0.82[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.82[ASN][1000 genomes]
rs2016161	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2067488	0.82[ASN][1000 genomes]
rs2254635	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.96[TSI][hapmap];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2405367	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]
rs2405392	0.81[CEU][hapmap];0.88[JPT][hapmap]
rs28703706	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2897119	0.89[EUR][1000 genomes]
rs3088162	0.90[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34374560	0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34746357	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34897231	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34911568	0.82[ASN][1000 genomes]
rs35488434	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35573837	0.81[ASN][1000 genomes]
rs35610040	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];0.97[ASN][1000 genomes]
rs35782710	0.82[ASN][1000 genomes]
rs35966482	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3761280	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3761281	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3787498	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]
rs3787499	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3810575	0.81[CEU][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap]
rs3827141	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];0.97[ASN][1000 genomes]
rs3827142	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];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3827143	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4346460	0.81[CEU][hapmap];0.88[JPT][hapmap]
rs4815222	0.81[CEU][hapmap];0.88[JPT][hapmap]
rs4815223	0.83[CEU][hapmap]
rs4815224	0.90[CEU][hapmap];0.82[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.82[ASN][1000 genomes]
rs5030707	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55897275	0.82[ASN][1000 genomes]
rs57549987	0.82[ASN][1000 genomes]
rs59059917	0.82[ASN][1000 genomes]
rs6036461	0.81[CEU][hapmap];0.88[JPT][hapmap]
rs6036465	0.81[CEU][hapmap];0.82[CHB][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.81[ASN][1000 genomes]
rs6036469	0.81[ASN][1000 genomes]
rs6036470	0.82[ASN][1000 genomes]
rs6036471	0.82[ASN][1000 genomes]
rs6036474	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6036476	0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6036478	0.85[CEU][hapmap];0.89[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6048920	0.81[CEU][hapmap];0.88[JPT][hapmap]
rs6048923	0.85[CEU][hapmap];0.88[JPT][hapmap]
rs6048928	0.85[CEU][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap]
rs6048929	0.81[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs6048930	0.85[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap]
rs6048933	0.82[ASN][1000 genomes]
rs6048936	0.81[ASN][1000 genomes]
rs6048945	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6048946	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6048949	0.81[ASN][1000 genomes]
rs6048950	0.83[ASN][1000 genomes]
rs6048952	0.85[CEU][hapmap];0.82[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6048956	0.90[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61035931	0.82[ASN][1000 genomes]
rs6114201	0.85[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6114206	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6114208	0.90[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6114209	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6515375	1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs67567111	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67997662	0.82[ASN][1000 genomes]
rs71334202	0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7265178	0.83[ASN][1000 genomes]
rs7270413	0.82[ASN][1000 genomes]
rs73318135	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs734801	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8114619	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8115417	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8115423	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8116859	0.85[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs8121147	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8121283	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8121405	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs911119	0.89[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2424582	CST3	cis	parietal	SCAN
rs2424582	CST3	cis	multi-tissue	Pritchard
rs2424582	CST3	cis	cerebellum	SCAN

Chromatin state (count:74 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:23618600-23622600	Weak transcription	Brain Anterior Caudate	brain
2	chr20:23618600-23622600	Weak transcription	Brain Substantia Nigra	brain
3	chr20:23618600-23622600	Weak transcription	Colon Smooth Muscle	Colon
4	chr20:23618600-23624800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr20:23618600-23626000	Weak transcription	Gastric	stomach
6	chr20:23618800-23622600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr20:23618800-23622600	Weak transcription	Right Atrium	heart
8	chr20:23618800-23623000	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr20:23618800-23623000	Weak transcription	NH-A	brain
10	chr20:23618800-23625200	Enhancers	Primary hematopoietic stem cells short term culture	blood
11	chr20:23618800-23626400	Weak transcription	Primary hematopoietic stem cells	blood
12	chr20:23618800-23628600	Enhancers	Primary monocytes fromperipheralblood	blood
13	chr20:23619200-23622600	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr20:23619400-23622800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr20:23619400-23623000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr20:23620000-23623200	Enhancers	Spleen	Spleen
17	chr20:23620000-23625000	Enhancers	Fetal Thymus	thymus
18	chr20:23620200-23623600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr20:23620600-23622800	Weak transcription	Colonic Mucosa	Colon
20	chr20:23620800-23623000	Enhancers	Thymus	Thymus
21	chr20:23620800-23623000	Weak transcription	HMEC	breast
22	chr20:23620800-23623000	Weak transcription	NHEK	skin
23	chr20:23620800-23623200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr20:23620800-23623400	Enhancers	ES-I3 Cell Line	embryonic stem cell
25	chr20:23620800-23624400	Enhancers	Fetal Muscle Leg	muscle
26	chr20:23621000-23622600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr20:23621000-23622800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr20:23621000-23623000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr20:23621200-23622800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
30	chr20:23621200-23622800	Weak transcription	Esophagus	oesophagus
31	chr20:23621200-23622800	Enhancers	Psoas Muscle	Psoas
32	chr20:23621200-23623400	Enhancers	Ovary	ovary
33	chr20:23621200-23623600	Enhancers	GM12878-XiMat	blood
34	chr20:23621200-23625200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr20:23621400-23623600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
36	chr20:23621400-23624800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr20:23621400-23625000	Enhancers	Adipose Nuclei	Adipose
38	chr20:23621600-23622600	Weak transcription	Duodenum Mucosa	Duodenum
39	chr20:23621600-23622800	Enhancers	Brain Cingulate Gyrus	brain
40	chr20:23621600-23623000	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
41	chr20:23621600-23623600	Enhancers	Brain Hippocampus Middle	brain
42	chr20:23621600-23623800	Enhancers	HSMM	muscle
43	chr20:23621800-23622800	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
44	chr20:23621800-23623000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr20:23621800-23623600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
46	chr20:23621800-23623800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr20:23621800-23624600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr20:23622000-23622600	Weak transcription	H1 Cell Line	embryonic stem cell
49	chr20:23622000-23622600	Enhancers	Stomach Smooth Muscle	stomach
50	chr20:23622000-23623000	Enhancers	iPS-20b Cell Line	embryonic stem cell

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