Variant report

Variant	rs6472216
Chromosome Location	chr8:66542277-66542278
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr8:66540600..66542392-chr8:66544818..66546528,2	MCF-7	breast:
2	chr8:66540570..66542467-chr8:66555055..66556755,2	MCF-7	breast:
3	chr8:66541684..66544207-chr8:66544873..66547787,2	K562	blood:

Variant related genes	Relation type
ENSG00000104442	Chromatin interaction

Extended variants
information (count: 115 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:114)

rs_ID	r²[population]
rs10087361	0.98[ASN][1000 genomes]
rs10089029	0.98[ASN][1000 genomes]
rs10089708	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10092109	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10097461	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10100131	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10110985	0.81[ASN][1000 genomes]
rs1053085	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1053087	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1053088	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10957361	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11776709	0.87[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs11776712	0.89[ASN][1000 genomes]
rs11985628	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11990855	0.97[ASN][1000 genomes]
rs12335006	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12335276	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12543053	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12544767	0.93[ASN][1000 genomes]
rs12677419	0.96[ASN][1000 genomes]
rs12678467	0.97[ASN][1000 genomes]
rs13252358	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13266834	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13267942	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13281155	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs14213	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1473601	0.98[ASN][1000 genomes]
rs1533285	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16932245	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16932250	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16932314	0.92[ASN][1000 genomes]
rs1877638	0.93[ASN][1000 genomes]
rs2048650	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2102648	0.95[ASN][1000 genomes]
rs2175809	0.96[ASN][1000 genomes]
rs2175810	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2357476	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28415299	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28576524	0.96[ASN][1000 genomes]
rs28613797	0.98[ASN][1000 genomes]
rs3268	0.97[ASN][1000 genomes]
rs34226237	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34494846	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34533611	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34851482	0.96[ASN][1000 genomes]
rs35038843	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35790435	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35941313	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3750184	0.97[ASN][1000 genomes]
rs3765205	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3812412	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4275254	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4320587	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4384016	0.88[AMR][1000 genomes]
rs4384017	0.82[ASN][1000 genomes]
rs4388482	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4397444	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4637885	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4637886	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4737222	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4737747	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4737748	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4737749	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4737750	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs5018458	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs57419568	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs60023200	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs60058315	0.97[ASN][1000 genomes]
rs6472213	0.97[ASN][1000 genomes]
rs6472214	0.86[ASN][1000 genomes]
rs6472215	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6472217	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6472218	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs66467166	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs66486920	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs67046768	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs67131486	0.93[ASN][1000 genomes]
rs67685675	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6985897	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6985932	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6986691	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6986866	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6991731	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6993876	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6994213	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6995242	0.97[ASN][1000 genomes]
rs6997959	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7006261	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7006648	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7007505	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7012578	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7012856	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7016472	0.97[ASN][1000 genomes]
rs71930161	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73236948	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73236986	0.98[ASN][1000 genomes]
rs73239011	0.98[ASN][1000 genomes]
rs73239085	0.97[ASN][1000 genomes]
rs7459737	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7464123	0.90[ASN][1000 genomes]
rs7464223	0.93[ASN][1000 genomes]
rs7812390	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7812446	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7814841	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7815488	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7817112	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7823840	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7832407	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7835313	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7836349	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7836746	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7841652	0.92[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs7842162	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7846527	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[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	esv2761434	chr8:65578467-66567678	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs6472216	CTD-3025N20.3	cis	Artery Tibial	GTEx
rs6472216	CTD-3025N20.3	cis	Esophagus Muscularis	GTEx
rs6472216	CTD-3025N20.3	cis	lung	GTEx
rs6472216	CTD-3025N20.3	cis	Thyroid	GTEx
rs6472216	CTD-3025N20.3	cis	Muscle Skeletal	GTEx

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:66504000-66545200	Weak transcription	Fetal Brain Male	brain
2	chr8:66506800-66545200	Weak transcription	Stomach Mucosa	stomach
3	chr8:66508000-66545200	Weak transcription	Fetal Heart	heart
4	chr8:66518000-66545600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr8:66519600-66545200	Weak transcription	Right Atrium	heart
6	chr8:66520000-66545000	Weak transcription	NHEK	skin
7	chr8:66522600-66545200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr8:66525600-66545200	Weak transcription	Fetal Kidney	kidney
9	chr8:66530200-66545000	Weak transcription	Hela-S3	cervix
10	chr8:66532000-66545600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr8:66532400-66545600	Weak transcription	Aorta	Aorta
12	chr8:66533600-66542600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr8:66533600-66545200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr8:66534000-66545200	Weak transcription	Brain Angular Gyrus	brain
15	chr8:66534200-66545200	Weak transcription	Colonic Mucosa	Colon
16	chr8:66534400-66545200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr8:66534600-66545200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr8:66535000-66544800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr8:66535000-66545200	Weak transcription	Brain Hippocampus Middle	brain
20	chr8:66535200-66545200	Weak transcription	Esophagus	oesophagus
21	chr8:66535200-66545600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr8:66536400-66543200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
23	chr8:66537600-66545200	Weak transcription	Gastric	stomach
24	chr8:66537800-66544800	Weak transcription	Placenta Amnion	Placenta Amnion
25	chr8:66537800-66545000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
26	chr8:66538000-66543800	Weak transcription	HSMM	muscle
27	chr8:66538000-66545200	Weak transcription	Colon Smooth Muscle	Colon
28	chr8:66538000-66545200	Weak transcription	NH-A	brain
29	chr8:66538200-66545000	Weak transcription	A549	lung
30	chr8:66538600-66545000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
31	chr8:66539000-66544800	Weak transcription	HMEC	breast
32	chr8:66539200-66545000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr8:66539200-66545000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
34	chr8:66539200-66545000	Weak transcription	Muscle Satellite Cultured Cells	--
35	chr8:66539200-66545200	Weak transcription	Rectal Smooth Muscle	rectum
36	chr8:66539400-66544800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr8:66539400-66545000	Weak transcription	Fetal Lung	lung
38	chr8:66539400-66545200	Weak transcription	Primary neutrophils fromperipheralblood	blood
39	chr8:66539400-66545200	Weak transcription	Brain Inferior Temporal Lobe	brain
40	chr8:66539600-66543400	Weak transcription	Fetal Stomach	stomach
41	chr8:66539600-66544400	Weak transcription	Brain Cingulate Gyrus	brain
42	chr8:66539600-66544400	Weak transcription	Sigmoid Colon	Sigmoid Colon
43	chr8:66539600-66544600	Weak transcription	Primary B cells from cord blood	blood
44	chr8:66539600-66544600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr8:66539600-66544800	Weak transcription	Brain Germinal Matrix	brain
46	chr8:66539600-66544800	Weak transcription	Fetal Intestine Large	intestine
47	chr8:66539600-66544800	Weak transcription	Lung	lung
48	chr8:66539600-66544800	Weak transcription	Psoas Muscle	Psoas
49	chr8:66539600-66545000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr8:66539600-66545000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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