Variant report

Variant	rs60439518
Chromosome Location	chr2:172314254-172314255
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	chr2:172289425..172291434-chr2:172312851..172315597,3	MCF-7	breast:
2	chr2:172308091..172309888-chr2:172313699..172316132,2	K562	blood:

Variant related genes	Relation type
ENSG00000123600	Chromatin interaction
ENSG00000115827	Chromatin interaction

Extended variants
information (count: 76 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs10445722	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10490604	0.80[EUR][1000 genomes]
rs10515933	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12151641	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1558936	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17220419	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17220440	0.98[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17220608	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17220657	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17220699	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17220734	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17221346	0.80[EUR][1000 genomes]
rs17221367	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17221402	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17221619	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17286415	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17286660	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1861899	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1981788	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2356781	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28742013	0.80[EUR][1000 genomes]
rs36112363	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3731981	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3731982	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3731983	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3731985	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3795998	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3821084	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4417688	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4458186	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4496302	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4522571	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4668385	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4668386	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4668387	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56410960	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs57099324	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs58536060	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs59960186	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs62181352	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs62183467	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62183468	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62183470	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs62183471	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs62183472	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62183492	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62183493	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62183494	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62183495	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62183497	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62183498	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62183499	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62183502	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62183503	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62183506	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62183507	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62183539	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6433290	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6433292	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6713612	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6720250	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6740733	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6741806	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6743290	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7568037	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7572334	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7576894	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7598137	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs7606658	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9678149	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9678164	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9679537	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9789572	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9789596	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3382346	chr2:172062677-172363892	Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
2	esv1832950	chr2:172283513-172488111	Flanking Active TSS Strong transcription Weak transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs60439518	CYBRD1	Cis_1M	lymphoblastoid	RTeQTL
rs60439518	METTL8	cis	Esophagus Muscularis	GTEx

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:172291000-172319800	Weak transcription	Stomach Mucosa	stomach
2	chr2:172291800-172338200	Weak transcription	Primary neutrophils fromperipheralblood	blood
3	chr2:172292000-172341600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr2:172292600-172317600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr2:172292600-172320400	Strong transcription	Primary T helper cells fromperipheralblood	blood
6	chr2:172293000-172318600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
7	chr2:172293200-172319400	Strong transcription	HUES6 Cell Line	embryonic stem cell
8	chr2:172293200-172319400	Strong transcription	HUES64 Cell Line	embryonic stem cell
9	chr2:172298200-172326600	Weak transcription	Colonic Mucosa	Colon
10	chr2:172298400-172325400	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr2:172298400-172325600	Weak transcription	Hela-S3	cervix
12	chr2:172298400-172326200	Weak transcription	NHEK	skin
13	chr2:172298400-172334400	Weak transcription	Small Intestine	intestine
14	chr2:172298400-172339400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr2:172298600-172341400	Weak transcription	NHLF	lung
16	chr2:172299400-172325400	Weak transcription	Gastric	stomach
17	chr2:172300600-172338600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
18	chr2:172303600-172316200	Strong transcription	Primary T helper cells PMA-I stimulated	--
19	chr2:172303600-172317000	Strong transcription	Primary B cells from peripheral blood	blood
20	chr2:172303800-172317400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr2:172304200-172316600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
22	chr2:172304200-172316800	Strong transcription	Liver	Liver
23	chr2:172304800-172314400	Weak transcription	Spleen	Spleen
24	chr2:172304800-172315400	Weak transcription	Fetal Intestine Small	intestine
25	chr2:172304800-172315600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr2:172304800-172315600	Weak transcription	Esophagus	oesophagus
27	chr2:172304800-172325200	Weak transcription	Brain Angular Gyrus	brain
28	chr2:172304800-172325200	Weak transcription	Pancreas	Pancrea
29	chr2:172304800-172330000	Weak transcription	NH-A	brain
30	chr2:172304800-172338800	Weak transcription	Placenta Amnion	Placenta Amnion
31	chr2:172305000-172326400	Weak transcription	Lung	lung
32	chr2:172305800-172325200	Weak transcription	Aorta	Aorta
33	chr2:172305800-172325400	Weak transcription	Brain Inferior Temporal Lobe	brain
34	chr2:172306000-172348000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
35	chr2:172306800-172325200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
36	chr2:172306800-172325800	Weak transcription	Rectal Smooth Muscle	rectum
37	chr2:172306800-172334000	Weak transcription	Psoas Muscle	Psoas
38	chr2:172307400-172325400	Weak transcription	Thymus	Thymus
39	chr2:172307600-172314400	Weak transcription	HSMMtube	muscle
40	chr2:172307600-172314800	Weak transcription	Brain Hippocampus Middle	brain
41	chr2:172307600-172325800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
42	chr2:172307600-172325800	Weak transcription	Colon Smooth Muscle	Colon
43	chr2:172307800-172325000	Weak transcription	Sigmoid Colon	Sigmoid Colon
44	chr2:172307800-172341200	Weak transcription	Right Ventricle	heart
45	chr2:172308200-172325800	Weak transcription	Brain Anterior Caudate	brain
46	chr2:172309400-172325800	Weak transcription	Stomach Smooth Muscle	stomach
47	chr2:172309600-172314400	Weak transcription	Muscle Satellite Cultured Cells	--
48	chr2:172309600-172314400	Weak transcription	HepG2	liver
49	chr2:172309600-172325400	Weak transcription	Brain Cingulate Gyrus	brain
50	chr2:172309600-172348400	Weak transcription	Fetal Heart	heart

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