Variant report

Variant	rs3827143
Chromosome Location	chr20:23619617-23619618
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	ZC3H11A	chr20:23619561-23619657	K562	blood:	n/a	n/a
2	FOXA2	chr20:23619552-23619851	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr20:23400787..23402892-chr20:23617355..23620191,2	MCF-7	breast:
2	chr20:23608610..23615599-chr20:23616056..23619619,19	MCF-7	breast:
3	chr20:23342009..23344759-chr20:23616093..23619702,3	MCF-7	breast:

Variant related genes	Relation type
CST3	TF binding region
ENSG00000125814	Chromatin interaction
ENSG00000270001	Chromatin interaction
ENSG00000125812	Chromatin interaction

Extended variants
information (count: 108 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs1010117	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];0.88[TSI][hapmap];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1064039	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1158167	0.85[CEU][hapmap];0.88[JPT][hapmap];0.81[TSI][hapmap];0.80[EUR][1000 genomes]
rs12624424	0.80[AMR][1000 genomes];0.88[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];0.88[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];0.90[TSI][hapmap];0.83[EUR][1000 genomes]
rs13038305	0.95[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];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];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13040663	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs13041070	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13043266	0.90[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.85[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];0.93[TSI][hapmap];0.85[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];0.88[TSI][hapmap];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2016161	0.98[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];0.93[TSI][hapmap];0.90[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];0.93[TSI][hapmap];0.90[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];0.97[TSI][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28703706	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2897119	0.82[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];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34374560	0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34746357	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34792920	0.82[EUR][1000 genomes]
rs34897231	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34911568	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs35488434	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35573837	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35610040	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.97[TSI][hapmap];0.83[YRI][hapmap];0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35782710	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs35966482	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3761280	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3761281	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3787498	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]
rs3787499	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.97[TSI][hapmap];0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3810575	0.86[CEU][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.80[EUR][1000 genomes]
rs3827141	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.97[TSI][hapmap];0.83[YRI][hapmap];0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3827142	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.97[TSI][hapmap];0.83[YRI][hapmap];0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4346460	0.86[CEU][hapmap];0.88[JPT][hapmap]
rs4815222	0.86[CEU][hapmap];0.88[JPT][hapmap];0.81[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];0.97[TSI][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs5030707	0.99[AFR][1000 genomes];0.94[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	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6036461	0.86[CEU][hapmap];0.88[JPT][hapmap];0.81[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];0.88[TSI][hapmap];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6036469	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6036470	0.80[AMR][1000 genomes];0.86[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	0.94[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];0.88[TSI][hapmap];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6048920	0.86[CEU][hapmap];0.88[JPT][hapmap];0.81[TSI][hapmap];0.80[EUR][1000 genomes]
rs6048922	0.80[EUR][1000 genomes]
rs6048923	0.90[CEU][hapmap];0.88[JPT][hapmap];0.83[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];0.93[TSI][hapmap];0.85[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	0.80[AMR][1000 genomes];0.86[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	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6048946	0.88[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];0.88[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];0.94[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	0.82[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];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6114209	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6515375	0.83[CEU][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs67567111	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67997662	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs71334202	0.84[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[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs734801	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8114619	0.88[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	0.88[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:5 , 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
3	esv3359195	chr20:23617352-23620750	Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
4	esv3377051	chr20:23617777-23620325	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
5	esv3336303	chr20:23617902-23620300	Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs3827143	CST3	cis	parietal	SCAN
rs3827143	CST3	cis	lymphoblastoid	seeQTL
rs3827143	CST3	cis	cerebellum	SCAN
rs3827143	CST3	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:82 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:23618600-23620000	Weak transcription	Rectal Mucosa Donor 29	rectum
2	chr20:23618600-23620000	Weak transcription	Skeletal Muscle Female	skeletal muscle
3	chr20:23618600-23620200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr20:23618600-23620400	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr20:23618600-23620800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr20:23618600-23621000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr20:23618600-23621200	Weak transcription	Ovary	ovary
8	chr20:23618600-23621200	Weak transcription	GM12878-XiMat	blood
9	chr20:23618600-23621600	Weak transcription	Liver	Liver
10	chr20:23618600-23621600	Weak transcription	Brain Hippocampus Middle	brain
11	chr20:23618600-23621800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr20:23618600-23621800	Weak transcription	Left Ventricle	heart
13	chr20:23618600-23622000	Weak transcription	HUVEC	blood vessel
14	chr20:23618600-23622200	Weak transcription	Muscle Satellite Cultured Cells	--
15	chr20:23618600-23622400	Weak transcription	Duodenum Smooth Muscle	Duodenum
16	chr20:23618600-23622400	Weak transcription	NHDF-Ad	bronchial
17	chr20:23618600-23622400	Weak transcription	NHLF	lung
18	chr20:23618600-23622600	Weak transcription	Brain Anterior Caudate	brain
19	chr20:23618600-23622600	Weak transcription	Brain Substantia Nigra	brain
20	chr20:23618600-23622600	Weak transcription	Colon Smooth Muscle	Colon
21	chr20:23618600-23624800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr20:23618600-23626000	Weak transcription	Gastric	stomach
23	chr20:23618800-23619800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
24	chr20:23618800-23620000	Enhancers	NHEK	skin
25	chr20:23618800-23620400	Enhancers	A549	lung
26	chr20:23618800-23620600	Weak transcription	Fetal Intestine Large	intestine
27	chr20:23618800-23620800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr20:23618800-23621000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr20:23618800-23621200	Weak transcription	H1 Cell Line	embryonic stem cell
30	chr20:23618800-23621200	Weak transcription	Psoas Muscle	Psoas
31	chr20:23618800-23621400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr20:23618800-23621400	Weak transcription	Primary B cells from cord blood	blood
33	chr20:23618800-23621400	Weak transcription	HSMMtube	muscle
34	chr20:23618800-23621600	Weak transcription	Brain Cingulate Gyrus	brain
35	chr20:23618800-23621600	Weak transcription	Pancreas	Pancrea
36	chr20:23618800-23621600	Weak transcription	HSMM	muscle
37	chr20:23618800-23621800	Enhancers	Monocytes-CD14+_RO01746	blood
38	chr20:23618800-23622000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr20:23618800-23622000	Enhancers	Placenta	Placenta
40	chr20:23618800-23622000	Weak transcription	Stomach Smooth Muscle	stomach
41	chr20:23618800-23622200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr20:23618800-23622400	Weak transcription	Fetal Lung	lung
43	chr20:23618800-23622400	Weak transcription	Osteobl	bone
44	chr20:23618800-23622600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr20:23618800-23622600	Weak transcription	Right Atrium	heart
46	chr20:23618800-23623000	Weak transcription	Placenta Amnion	Placenta Amnion
47	chr20:23618800-23623000	Weak transcription	NH-A	brain
48	chr20:23618800-23625200	Enhancers	Primary hematopoietic stem cells short term culture	blood
49	chr20:23618800-23626400	Weak transcription	Primary hematopoietic stem cells	blood
50	chr20:23618800-23628600	Enhancers	Primary monocytes fromperipheralblood	blood

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