Variant report

Variant	rs12625716
Chromosome Location	chr20:23606845-23606846
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr20:23603693..23605548-chr20:23605615..23607306,2	MCF-7	breast:
2	chr20:23605616..23608298-chr20:23618129..23620935,3	MCF-7	breast:
3	chr20:23606151..23608595-chr20:23610355..23612719,2	K562	blood:
4	chr20:23604645..23607070-chr20:23613987..23616956,2	K562	blood:
5	chr20:23606151..23607928-chr20:23610355..23613024,2	K562	blood:

Variant related genes	Relation type
ENSG00000270001	Chromatin interaction
ENSG00000101439	Chromatin interaction

Extended variants
information (count: 110 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:109)

rs_ID	r²[population]
rs1010117	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1011226	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1064039	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1158167	0.95[CEU][hapmap];0.90[CHB][hapmap];0.84[CHD][hapmap];0.88[JPT][hapmap];0.94[TSI][hapmap];0.88[EUR][1000 genomes]
rs12624424	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12625182	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12710327	0.84[EUR][1000 genomes]
rs13037490	0.90[CEU][hapmap];0.90[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap];0.84[EUR][1000 genomes]
rs13038305	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13038337	0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13038990	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13039536	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13040663	0.80[EUR][1000 genomes]
rs13041070	0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13043266	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13043610	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1555355	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17751897	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2016161	0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2067488	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2208289	0.88[EUR][1000 genomes]
rs2254635	0.84[CEU][hapmap];0.82[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2405367	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]
rs2405392	0.95[CEU][hapmap];0.90[CHB][hapmap];0.88[JPT][hapmap];0.83[EUR][1000 genomes]
rs2405393	0.83[EUR][1000 genomes]
rs2424582	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]
rs28703706	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3004139	0.88[EUR][1000 genomes]
rs3004145	0.88[EUR][1000 genomes]
rs3088162	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34374560	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34746357	0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34792920	0.83[EUR][1000 genomes]
rs34897231	0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34911568	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35488434	0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35573837	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35610040	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];0.92[ASN][1000 genomes]
rs35782710	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35966482	0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3761280	0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3761281	0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3787498	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]
rs3787499	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];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3810575	0.95[CEU][hapmap];0.90[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.94[TSI][hapmap];0.88[EUR][1000 genomes]
rs3827141	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];0.92[ASN][1000 genomes]
rs3827142	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]
rs3827143	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]
rs4346460	0.95[CEU][hapmap];0.90[CHB][hapmap];0.88[JPT][hapmap];0.89[MEX][hapmap];0.91[TSI][hapmap];0.83[EUR][1000 genomes]
rs4815222	0.95[CEU][hapmap];0.90[CHB][hapmap];0.84[CHD][hapmap];0.88[JPT][hapmap];0.89[MEX][hapmap];0.94[TSI][hapmap];0.88[EUR][1000 genomes]
rs4815223	0.94[CEU][hapmap];0.88[EUR][1000 genomes]
rs4815224	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.88[MEX][hapmap];0.91[TSI][hapmap];0.80[YRI][hapmap];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs5030707	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs55897275	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs56077567	0.81[EUR][1000 genomes]
rs56371840	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs56388902	0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs57549987	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs59059917	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6036461	0.95[CEU][hapmap];0.90[CHB][hapmap];0.84[CHD][hapmap];0.88[JPT][hapmap];0.89[MEX][hapmap];0.94[TSI][hapmap];0.88[EUR][1000 genomes]
rs6036463	0.88[EUR][1000 genomes]
rs6036465	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6036469	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6036470	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6036471	0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6036474	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6036476	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6036478	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6048920	0.95[CEU][hapmap];0.90[CHB][hapmap];0.84[CHD][hapmap];0.88[JPT][hapmap];0.89[MEX][hapmap];0.94[TSI][hapmap];0.88[EUR][1000 genomes]
rs6048922	0.88[EUR][1000 genomes]
rs6048923	0.90[CEU][hapmap];0.90[CHB][hapmap];0.88[JPT][hapmap];0.84[EUR][1000 genomes]
rs6048924	0.88[EUR][1000 genomes]
rs6048925	0.87[EUR][1000 genomes]
rs6048926	0.87[EUR][1000 genomes]
rs6048928	0.90[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6048929	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6048930	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6048933	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6048936	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6048939	0.83[EUR][1000 genomes]
rs6048941	0.86[EUR][1000 genomes]
rs6048945	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6048946	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6048949	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6048950	0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6048952	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6048956	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61035931	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6106685	0.87[EUR][1000 genomes]
rs6114201	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6114206	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6114208	0.85[CEU][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6114209	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6515375	0.84[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs67567111	0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs67997662	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs71334202	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7265178	0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7270413	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73318135	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs734801	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8114619	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8115417	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8115423	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8116859	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8121147	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8121283	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8121405	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs911119	0.95[CEU][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[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
rs12625716	CST3	cis	parietal	SCAN
rs12625716	CST3	cis	cerebellum	SCAN
rs12625716	CST3	cis	multi-tissue	Pritchard

Chromatin state (count:78 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:23600600-23617000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr20:23602000-23609400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr20:23602000-23610000	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr20:23602000-23610200	Weak transcription	Lung	lung
5	chr20:23602000-23612200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr20:23602000-23616800	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr20:23603800-23609200	Weak transcription	Fetal Muscle Trunk	muscle
8	chr20:23603800-23609800	Weak transcription	Fetal Thymus	thymus
9	chr20:23603800-23615400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr20:23604000-23607200	Enhancers	HepG2	liver
11	chr20:23604000-23607400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr20:23604000-23607400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr20:23604000-23608800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr20:23604000-23608800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr20:23604000-23609600	Weak transcription	Rectal Mucosa Donor 29	rectum
16	chr20:23604000-23610200	Weak transcription	Ovary	ovary
17	chr20:23604000-23612200	Weak transcription	Liver	Liver
18	chr20:23604000-23612800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr20:23604000-23613000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr20:23604000-23613000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr20:23604000-23613400	Weak transcription	Brain Hippocampus Middle	brain
22	chr20:23604000-23614400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
23	chr20:23604000-23616600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
24	chr20:23604000-23616800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr20:23604200-23607200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr20:23604200-23607600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr20:23604200-23607600	Enhancers	HMEC	breast
28	chr20:23604200-23607600	Enhancers	NHEK	skin
29	chr20:23604200-23609200	Weak transcription	HUVEC	blood vessel
30	chr20:23604200-23609200	Weak transcription	Osteobl	bone
31	chr20:23604200-23609800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
32	chr20:23604200-23610000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr20:23604200-23615000	Weak transcription	Brain Anterior Caudate	brain
34	chr20:23604800-23608800	Weak transcription	Left Ventricle	heart
35	chr20:23604800-23609000	Weak transcription	Fetal Intestine Small	intestine
36	chr20:23604800-23612200	Weak transcription	Aorta	Aorta
37	chr20:23605000-23607000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr20:23605000-23607200	Enhancers	GM12878-XiMat	blood
39	chr20:23605000-23609200	Weak transcription	Adipose Nuclei	Adipose
40	chr20:23605000-23611800	Weak transcription	Fetal Muscle Leg	muscle
41	chr20:23605000-23612800	Weak transcription	Rectal Smooth Muscle	rectum
42	chr20:23605200-23612200	Weak transcription	NHLF	lung
43	chr20:23605400-23609600	Weak transcription	Muscle Satellite Cultured Cells	--
44	chr20:23605400-23612200	Weak transcription	Stomach Smooth Muscle	stomach
45	chr20:23605800-23607000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
46	chr20:23605800-23607600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr20:23606000-23609600	Weak transcription	NHDF-Ad	bronchial
48	chr20:23606200-23607400	Enhancers	Cortex derived primary cultured neurospheres	brain
49	chr20:23606400-23607000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr20:23606400-23607000	Enhancers	Colon Smooth Muscle	Colon

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