Variant report

Variant	rs4562925
Chromosome Location	chr12:117362453-117362454
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:117356635..117358381-chr12:117361006..117362660,2	K562	blood:
2	chr12:117349947..117352255-chr12:117362016..117363854,2	K562	blood:

Extended variants
information (count: 103 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:100)

rs_ID	r²[population]
rs10507277	0.86[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10732611	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10735099	0.87[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10735102	0.87[CEU][hapmap];0.86[JPT][hapmap];0.84[MEX][hapmap];0.81[TSI][hapmap]
rs10735103	0.93[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10744885	0.88[ASN][1000 genomes]
rs10744886	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10774891	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap]
rs10774892	0.94[CHB][hapmap];1.00[JPT][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10774893	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10774896	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10850731	0.85[CEU][hapmap];0.85[JPT][hapmap];0.82[EUR][1000 genomes]
rs10850733	0.96[EUR][1000 genomes]
rs10850741	0.92[EUR][1000 genomes]
rs10850743	0.87[CEU][hapmap];0.88[CHB][hapmap];0.89[CHD][hapmap];0.86[JPT][hapmap];0.86[TSI][hapmap];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10850744	1.00[CEU][hapmap];0.94[CHB][hapmap];0.84[JPT][hapmap]
rs11068247	0.84[JPT][hapmap]
rs11068258	0.84[JPT][hapmap]
rs11068262	0.84[JPT][hapmap]
rs11068264	0.87[CEU][hapmap];0.86[JPT][hapmap];0.83[MEX][hapmap];0.81[TSI][hapmap]
rs11068277	0.87[CEU][hapmap];0.86[JPT][hapmap];0.81[TSI][hapmap]
rs11068280	0.91[JPT][hapmap]
rs11068282	0.81[CHD][hapmap];0.84[JPT][hapmap]
rs11068286	0.83[JPT][hapmap]
rs11068296	0.87[CEU][hapmap];0.94[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap];0.87[ASN][1000 genomes]
rs12299065	0.86[CEU][hapmap];0.95[GIH][hapmap];0.96[TSI][hapmap];0.90[EUR][1000 genomes]
rs12821492	0.91[ASN][1000 genomes]
rs17583145	0.82[JPT][hapmap]
rs17616662	0.84[JPT][hapmap]
rs2242469	0.86[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs2393110	0.81[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2393111	0.93[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.86[TSI][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35833140	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3803089	0.84[JPT][hapmap]
rs3893370	0.93[CEU][hapmap];0.94[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.82[TSI][hapmap];0.89[ASN][1000 genomes]
rs4074147	0.94[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4076700	0.93[CEU][hapmap];0.88[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.86[TSI][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4077519	0.88[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4130296	1.00[ASW][hapmap];1.00[CEU][hapmap];0.81[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4238051	0.86[CEU][hapmap];0.95[GIH][hapmap];0.96[TSI][hapmap];0.96[EUR][1000 genomes]
rs4299000	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4324001	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4347476	0.84[JPT][hapmap]
rs4522274	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4542506	0.93[CEU][hapmap];0.81[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.86[TSI][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4562926	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4562927	0.87[CEU][hapmap];0.86[JPT][hapmap];0.84[MEX][hapmap];0.81[TSI][hapmap];0.82[EUR][1000 genomes]
rs4766812	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4766814	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4766815	0.87[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.86[TSI][hapmap];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4766818	0.83[YRI][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4766820	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4766821	0.87[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4766822	0.86[JPT][hapmap]
rs4767473	0.95[GIH][hapmap];0.81[MEX][hapmap];0.96[TSI][hapmap];0.96[EUR][1000 genomes]
rs4767474	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.86[TSI][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4767476	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4767478	0.93[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4767480	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4767482	0.94[CHB][hapmap];0.92[JPT][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4767483	0.93[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.86[TSI][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4767484	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.86[TSI][hapmap];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4767485	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4767487	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4767488	1.00[CHB][hapmap];0.92[JPT][hapmap];0.88[ASN][1000 genomes]
rs4767489	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.86[TSI][hapmap];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4767490	0.86[CEU][hapmap];0.89[GIH][hapmap];0.96[TSI][hapmap];0.92[EUR][1000 genomes]
rs4767491	0.92[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4767493	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs60940473	0.90[EUR][1000 genomes]
rs6490097	0.85[ASN][1000 genomes]
rs6490102	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7131746	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7133066	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs7136629	0.84[JPT][hapmap]
rs7137006	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7137752	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7297155	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7297848	0.87[CEU][hapmap];0.86[JPT][hapmap]
rs7297934	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7298447	1.00[CEU][hapmap];0.94[CHB][hapmap];0.92[JPT][hapmap];0.83[YRI][hapmap];0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7302025	0.86[CEU][hapmap];0.95[GIH][hapmap];0.96[TSI][hapmap];0.90[EUR][1000 genomes]
rs7303752	0.87[EUR][1000 genomes]
rs7303882	0.88[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7307907	0.93[EUR][1000 genomes]
rs7308498	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7311972	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.91[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7312388	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7316144	0.86[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7484620	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7487081	1.00[JPT][hapmap]
rs7952766	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7954824	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7957907	0.90[EUR][1000 genomes]
rs7958030	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7959666	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7973240	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7976815	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7977598	0.87[ASN][1000 genomes]
rs9804817	0.85[CEU][hapmap];0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832524	chr12:117314110-117496576	Weak transcription Strong transcription Enhancers ZNF genes & repeats Bivalent Enhancer Genic enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv1046811	chr12:117353904-117396230	Weak transcription ZNF genes & repeats Genic enhancers Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	Chromatin interactive region	5 gene(s)	inside rSNPs	n/a
3	esv1798657	chr12:117354067-117392259	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	5 gene(s)	inside rSNPs	n/a

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4562925	TESC	cis	lymphoblastoid	seeQTL
rs4562925	TESC	cis	parietal	SCAN
rs4562925	FBXW8	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:117349600-117363600	Weak transcription	Brain Anterior Caudate	brain
2	chr12:117349600-117364000	Weak transcription	Brain Angular Gyrus	brain
3	chr12:117349600-117365800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr12:117349800-117363600	Weak transcription	Brain Substantia Nigra	brain
5	chr12:117349800-117363800	Weak transcription	Aorta	Aorta
6	chr12:117349800-117364000	Weak transcription	Adipose Nuclei	Adipose
7	chr12:117349800-117366000	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr12:117349800-117366000	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr12:117349800-117366000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr12:117349800-117371000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr12:117350000-117363000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
12	chr12:117350000-117363800	Weak transcription	Brain Hippocampus Middle	brain
13	chr12:117350000-117365400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
14	chr12:117350000-117366000	Weak transcription	Fetal Lung	lung
15	chr12:117350200-117366000	Weak transcription	Stomach Smooth Muscle	stomach
16	chr12:117350200-117366000	Weak transcription	Monocytes-CD14+_RO01746	blood
17	chr12:117350200-117366800	Weak transcription	Spleen	Spleen
18	chr12:117350200-117367800	Weak transcription	Brain Germinal Matrix	brain
19	chr12:117350200-117371000	Weak transcription	Right Ventricle	heart
20	chr12:117350600-117370600	Weak transcription	Fetal Brain Male	brain
21	chr12:117351200-117363800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr12:117352400-117364200	Weak transcription	Fetal Stomach	stomach
23	chr12:117354600-117362800	Weak transcription	HUES64 Cell Line	embryonic stem cell
24	chr12:117354800-117362600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr12:117354800-117363000	Weak transcription	Left Ventricle	heart
26	chr12:117354800-117383200	Weak transcription	Esophagus	oesophagus
27	chr12:117355000-117363000	Weak transcription	Skeletal Muscle Female	skeletal muscle
28	chr12:117355600-117362800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr12:117355600-117363000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr12:117355600-117365400	Weak transcription	Lung	lung
31	chr12:117356600-117364000	Weak transcription	Ovary	ovary
32	chr12:117357000-117365800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
33	chr12:117357200-117364400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
34	chr12:117357200-117365400	Weak transcription	Placenta	Placenta
35	chr12:117357200-117365600	Weak transcription	Rectal Mucosa Donor 29	rectum
36	chr12:117357200-117367600	Weak transcription	Primary monocytes fromperipheralblood	blood
37	chr12:117357400-117365400	Weak transcription	Fetal Muscle Trunk	muscle
38	chr12:117357600-117363000	Weak transcription	Placenta Amnion	Placenta Amnion
39	chr12:117357600-117363600	Weak transcription	Right Atrium	heart
40	chr12:117357600-117365000	Weak transcription	Fetal Muscle Leg	muscle
41	chr12:117357800-117367600	Weak transcription	Fetal Heart	heart
42	chr12:117358000-117366000	Weak transcription	Liver	Liver
43	chr12:117358400-117363000	Weak transcription	Skeletal Muscle Male	skeletal muscle
44	chr12:117358400-117365600	Enhancers	Primary T cells fromperipheralblood	blood
45	chr12:117358400-117366000	Weak transcription	Fetal Intestine Large	intestine
46	chr12:117358400-117366000	Weak transcription	Fetal Kidney	kidney
47	chr12:117358400-117392600	Weak transcription	Small Intestine	intestine
48	chr12:117358600-117362600	Enhancers	Primary T killer memory cells from peripheral blood	blood
49	chr12:117358600-117363600	Weak transcription	Fetal Brain Female	brain
50	chr12:117358600-117365000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood

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