Variant report

Variant	rs6114209
Chromosome Location	chr20:23622266-23622267
allele	C/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	chr20:23622200-23622350	HepG2	liver:	n/a	n/a
2	CTCF	chr20:23622217-23622278	GM12891	blood:	n/a	n/a
3	NR2F2	chr20:23621694-23622374	HepG2	liver:	n/a	n/a
4	CTCF	chr20:23622140-23622290	HCPEpiC	choroid plexus:	n/a	n/a
5	EP300	chr20:23621762-23622311	HepG2	liver:	n/a	chr20:23621979-23621993 chr20:23621940-23621956
6	CTCF	chr20:23622160-23622310	HepG2	liver:	n/a	n/a
7	FOXA1	chr20:23621717-23622306	HepG2	liver:	n/a	n/a
8	RAD21	chr20:23621752-23622334	HepG2	liver:	n/a	n/a
9	CTCF	chr20:23622140-23622290	GM12872	blood:	n/a	n/a
10	MAZ	chr20:23621607-23622306	HepG2	liver:	n/a	n/a
11	FOXA2	chr20:23621843-23622322	HepG2	liver:	n/a	n/a
12	CTCF	chr20:23622187-23622322	HepG2	liver:	n/a	n/a
13	CTCF	chr20:23622140-23622290	GM12867	blood:	n/a	n/a
14	CTCF	chr20:23622133-23622359	HepG2	liver:	n/a	n/a
15	ELF1	chr20:23621839-23622327	HepG2	liver:	n/a	chr20:23621978-23621989
16	HDAC2	chr20:23621650-23622329	HepG2	liver:	n/a	n/a
17	EP300	chr20:23621918-23622561	HepG2	liver:	n/a	chr20:23621979-23621993 chr20:23621940-23621956
18	MAX	chr20:23621638-23622398	HepG2	liver:	n/a	n/a
19	CTCF	chr20:23622220-23622370	HBMEC	blood vessel:	n/a	n/a
20	CTCF	chr20:23622140-23622290	HFF-Myc	foreskin:	n/a	n/a
21	MYBL2	chr20:23621583-23622396	HepG2	liver:	n/a	n/a
22	CEBPB	chr20:23621800-23622359	HepG2	liver:	n/a	n/a
23	CTCF	chr20:23622120-23622270	GM12875	blood:	n/a	n/a
24	SMC3	chr20:23621912-23622402	HepG2	liver:	n/a	chr20:23622256-23622266
25	ARID3A	chr20:23621811-23622269	HepG2	liver:	n/a	n/a
26	RAD21	chr20:23621959-23622449	HepG2	liver:	n/a	n/a
27	CTCF	chr20:23622160-23622310	WERI-Rb-1	eye:	n/a	n/a
28	MYBL2	chr20:23620530-23622392	HepG2	liver:	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: 89 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:88)

rs_ID	r²[population]
rs1010117	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1011226	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1064039	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12624424	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12625182	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12625716	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13037490	0.82[EUR][1000 genomes]
rs13038305	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13038337	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13038990	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13039536	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13040663	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs13041070	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13043266	0.85[EUR][1000 genomes]
rs13043610	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1555355	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17751897	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2016161	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2067488	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2254635	0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2405367	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2424582	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28703706	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2897119	0.83[EUR][1000 genomes]
rs3088162	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34374560	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34746357	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34792920	0.81[EUR][1000 genomes]
rs34897231	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34911568	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs35488434	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35573837	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35610040	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35782710	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs35966482	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3761280	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3761281	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3787498	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3787499	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3827141	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3827142	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3827143	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4815224	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs5030707	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55897275	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs56371840	0.84[EUR][1000 genomes]
rs56388902	0.83[EUR][1000 genomes]
rs57549987	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs59059917	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6036465	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6036469	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6036470	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6036471	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6036474	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6036476	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6036478	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6048923	0.82[EUR][1000 genomes]
rs6048928	0.84[EUR][1000 genomes]
rs6048929	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6048933	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6048936	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6048941	0.81[EUR][1000 genomes]
rs6048945	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6048946	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6048949	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6048950	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6048952	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6048956	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61035931	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6114201	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6114206	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6114208	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6515375	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs67567111	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67997662	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs71334202	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7265178	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7270413	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs73318135	0.93[AMR][1000 genomes];0.96[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	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8115417	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8115423	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8116859	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8121147	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8121283	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8121405	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs911119	0.93[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6114209	CST3	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:23618600-23622400	Weak transcription	Duodenum Smooth Muscle	Duodenum
2	chr20:23618600-23622400	Weak transcription	NHDF-Ad	bronchial
3	chr20:23618600-23622400	Weak transcription	NHLF	lung
4	chr20:23618600-23622600	Weak transcription	Brain Anterior Caudate	brain
5	chr20:23618600-23622600	Weak transcription	Brain Substantia Nigra	brain
6	chr20:23618600-23622600	Weak transcription	Colon Smooth Muscle	Colon
7	chr20:23618600-23624800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr20:23618600-23626000	Weak transcription	Gastric	stomach
9	chr20:23618800-23622400	Weak transcription	Fetal Lung	lung
10	chr20:23618800-23622400	Weak transcription	Osteobl	bone
11	chr20:23618800-23622600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr20:23618800-23622600	Weak transcription	Right Atrium	heart
13	chr20:23618800-23623000	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr20:23618800-23623000	Weak transcription	NH-A	brain
15	chr20:23618800-23625200	Enhancers	Primary hematopoietic stem cells short term culture	blood
16	chr20:23618800-23626400	Weak transcription	Primary hematopoietic stem cells	blood
17	chr20:23618800-23628600	Enhancers	Primary monocytes fromperipheralblood	blood
18	chr20:23619000-23622400	Flanking Active TSS	HepG2	liver
19	chr20:23619200-23622600	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr20:23619400-23622800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr20:23619400-23623000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr20:23620000-23623200	Enhancers	Spleen	Spleen
23	chr20:23620000-23625000	Enhancers	Fetal Thymus	thymus
24	chr20:23620200-23623600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr20:23620600-23622800	Weak transcription	Colonic Mucosa	Colon
26	chr20:23620800-23623000	Enhancers	Thymus	Thymus
27	chr20:23620800-23623000	Weak transcription	HMEC	breast
28	chr20:23620800-23623000	Weak transcription	NHEK	skin
29	chr20:23620800-23623200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr20:23620800-23623400	Enhancers	ES-I3 Cell Line	embryonic stem cell
31	chr20:23620800-23624400	Enhancers	Fetal Muscle Leg	muscle
32	chr20:23621000-23622600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr20:23621000-23622800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr20:23621000-23623000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr20:23621200-23622800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
36	chr20:23621200-23622800	Weak transcription	Esophagus	oesophagus
37	chr20:23621200-23622800	Enhancers	Psoas Muscle	Psoas
38	chr20:23621200-23623400	Enhancers	Ovary	ovary
39	chr20:23621200-23623600	Enhancers	GM12878-XiMat	blood
40	chr20:23621200-23625200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
41	chr20:23621400-23623600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
42	chr20:23621400-23624800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr20:23621400-23625000	Enhancers	Adipose Nuclei	Adipose
44	chr20:23621600-23622400	Weak transcription	HUES64 Cell Line	embryonic stem cell
45	chr20:23621600-23622600	Weak transcription	Duodenum Mucosa	Duodenum
46	chr20:23621600-23622800	Enhancers	Brain Cingulate Gyrus	brain
47	chr20:23621600-23623000	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
48	chr20:23621600-23623600	Enhancers	Brain Hippocampus Middle	brain
49	chr20:23621600-23623800	Enhancers	HSMM	muscle
50	chr20:23621800-23622800	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle

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