Variant report

Variant	rs60663580
Chromosome Location	chr5:74090336-74090337
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:74070106..74071963-chr5:74087987..74090742,2	K562	blood:

Extended variants
information (count: 117 )
Associated
traits (count: 14 )

rSNPs within LD-proxies of this variant (count:116)

rs_ID	r²[population]
rs1043968	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10515191	0.89[EUR][1000 genomes]
rs10515192	0.93[AFR][1000 genomes]
rs10515194	0.93[AFR][1000 genomes]
rs1104272	0.81[EUR][1000 genomes]
rs11739122	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11741789	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11741825	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11742460	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11742621	0.81[EUR][1000 genomes]
rs11742773	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11743655	0.83[EUR][1000 genomes]
rs11746702	0.84[EUR][1000 genomes]
rs11746757	0.81[EUR][1000 genomes]
rs11747965	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11749137	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11948188	0.89[EUR][1000 genomes]
rs11955898	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1350097	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1447453	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs15694	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs16872220	0.86[AFR][1000 genomes]
rs16872231	0.85[AFR][1000 genomes]
rs16872297	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs16872299	0.87[EUR][1000 genomes]
rs16872333	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16872346	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs16872347	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16872364	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1812122	0.81[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs1993370	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2044410	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2061162	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2084115	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2084116	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2084118	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2100033	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2166361	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2314936	0.89[EUR][1000 genomes]
rs2314937	0.89[EUR][1000 genomes]
rs34496480	0.87[EUR][1000 genomes]
rs3733794	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4425487	0.85[ASN][1000 genomes]
rs4594835	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs5020673	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs55870102	0.89[EUR][1000 genomes]
rs56068548	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56202905	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56276104	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs56365996	0.89[EUR][1000 genomes]
rs57549677	0.86[AFR][1000 genomes]
rs58367004	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs59110717	0.89[EUR][1000 genomes]
rs62366408	0.89[EUR][1000 genomes]
rs62366414	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62366417	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62366423	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62366424	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62366426	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62366455	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62366458	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62367762	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62367766	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62367767	0.81[ASN][1000 genomes]
rs6453075	0.83[EUR][1000 genomes]
rs6453076	0.85[AFR][1000 genomes]
rs6453077	0.83[EUR][1000 genomes]
rs6453079	0.87[AFR][1000 genomes]
rs6453084	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6453086	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6453087	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6859014	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6861730	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6863738	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6866082	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6870806	0.92[AFR][1000 genomes]
rs6873067	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6873912	0.92[AFR][1000 genomes]
rs6873998	0.90[AFR][1000 genomes]
rs6874094	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6874609	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6877116	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6877188	0.85[AFR][1000 genomes]
rs6877442	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6879781	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6882035	0.93[AFR][1000 genomes]
rs6882499	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6883061	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6883278	0.92[AFR][1000 genomes]
rs6883420	0.92[AFR][1000 genomes]
rs6884338	0.91[AFR][1000 genomes]
rs6884843	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6885093	0.84[EUR][1000 genomes]
rs6885675	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6890815	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6894177	0.86[AFR][1000 genomes]
rs6897698	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6897904	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6898684	0.92[AFR][1000 genomes]
rs72764643	0.86[AFR][1000 genomes]
rs72764647	0.87[AFR][1000 genomes]
rs72764648	0.84[AFR][1000 genomes]
rs72764654	0.93[AFR][1000 genomes]
rs72764656	0.93[AFR][1000 genomes]
rs72764657	0.92[AFR][1000 genomes]
rs72764666	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs73120619	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7705519	0.91[AFR][1000 genomes]
rs7708203	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7713812	0.86[AFR][1000 genomes]
rs7717223	0.94[ASN][1000 genomes]
rs7724292	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7728889	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7732440	0.87[AFR][1000 genomes]
rs7732843	0.84[AFR][1000 genomes]
rs9686657	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[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	nsv598653	chr5:73992881-74095542	Active TSS Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:14)

SNP	Gene	Cis/trans	Tissue	Source
rs60663580	NSA2	cis	Esophagus Mucosa	GTEx
rs60663580	NSA2	cis	Nerve Tibial	GTEx
rs60663580	NSA2	cis	Muscle Skeletal	GTEx
rs60663580	NSA2	cis	Esophagus Muscularis	GTEx
rs60663580	NSA2	cis	Skin Sun Exposed Lower leg	GTEx
rs60663580	NSA2	cis	Thyroid	GTEx
rs60663580	NSA2	cis	Whole Blood	GTEx
rs60663580	NSA2	cis	lung	GTEx
rs60663580	NSA2	cis	Stomach	GTEx
rs60663580	NSA2	cis	Heart Left Ventricle	GTEx
rs60663580	NSA2	cis	Artery Tibial	GTEx
rs60663580	TINP1	Cis_1M	lymphoblastoid	RTeQTL
rs60663580	NSA2	cis	Adipose Subcutaneous	GTEx
rs60663580	NSA2	cis	Artery Aorta	GTEx

Chromatin state (count:76 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:74064000-74112400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr5:74064200-74102000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr5:74064400-74134600	Weak transcription	Fetal Brain Male	brain
4	chr5:74064800-74101200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
5	chr5:74066600-74112800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
6	chr5:74069000-74153000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr5:74069600-74102600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
8	chr5:74069800-74097000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
9	chr5:74070000-74095000	Weak transcription	Fetal Kidney	kidney
10	chr5:74070000-74097000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr5:74070000-74111600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
12	chr5:74071400-74095200	Weak transcription	Spleen	Spleen
13	chr5:74072400-74095600	Weak transcription	Left Ventricle	heart
14	chr5:74074200-74102600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
15	chr5:74074800-74094600	Weak transcription	HSMM	muscle
16	chr5:74074800-74097200	Weak transcription	Rectal Mucosa Donor 29	rectum
17	chr5:74074800-74097400	Weak transcription	Liver	Liver
18	chr5:74074800-74102200	Weak transcription	Primary B cells from peripheral blood	blood
19	chr5:74074800-74143400	Weak transcription	Primary B cells from cord blood	blood
20	chr5:74076400-74095400	Weak transcription	Cortex derived primary cultured neurospheres	brain
21	chr5:74079200-74091400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr5:74079400-74095000	Weak transcription	HMEC	breast
23	chr5:74081200-74101200	Strong transcription	HUES64 Cell Line	embryonic stem cell
24	chr5:74081200-74101200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
25	chr5:74081400-74097800	Strong transcription	H9 Cell Line	embryonic stem cell
26	chr5:74081400-74101400	Strong transcription	HUES6 Cell Line	embryonic stem cell
27	chr5:74081600-74098000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr5:74081600-74098600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr5:74081800-74101200	Strong transcription	HUES48 Cell Line	embryonic stem cell
30	chr5:74082400-74097800	Strong transcription	H1 Cell Line	embryonic stem cell
31	chr5:74083200-74098000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr5:74084200-74095400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr5:74085800-74098000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr5:74086000-74091200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
35	chr5:74086600-74097400	Weak transcription	Aorta	Aorta
36	chr5:74087000-74095200	Weak transcription	Fetal Stomach	stomach
37	chr5:74087000-74097000	Weak transcription	Brain Germinal Matrix	brain
38	chr5:74087200-74094000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
39	chr5:74087200-74094600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
40	chr5:74087200-74094600	Weak transcription	Brain Substantia Nigra	brain
41	chr5:74087200-74094800	Weak transcription	Brain Inferior Temporal Lobe	brain
42	chr5:74087200-74095400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
43	chr5:74087200-74096400	Weak transcription	Fetal Brain Female	brain
44	chr5:74087400-74094800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
45	chr5:74087600-74112000	Weak transcription	A549	lung
46	chr5:74087600-74130000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
47	chr5:74087800-74092600	Weak transcription	Primary hematopoietic stem cells	blood
48	chr5:74088200-74093400	Weak transcription	NHEK	skin
49	chr5:74088400-74090400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr5:74088400-74090600	Weak transcription	Brain Anterior Caudate	brain

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