Variant report

Variant	rs62302961
Chromosome Location	chr4:77113403-77113404
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:77108730..77110793-chr4:77112512..77115192,2	K562	blood:
2	chr4:77112114..77114114-chr4:77116048..77119897,3	K562	blood:

Variant related genes	Relation type
ENSG00000138760	Chromatin interaction

Extended variants
information (count: 170 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:168)

rs_ID	r²[population]
rs1051326	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1078350	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11097244	0.82[EUR][1000 genomes]
rs11558468	0.82[EUR][1000 genomes]
rs11558469	0.82[EUR][1000 genomes]
rs11722957	0.82[EUR][1000 genomes]
rs11724260	0.82[EUR][1000 genomes]
rs11725016	0.82[EUR][1000 genomes]
rs11727718	0.82[EUR][1000 genomes]
rs11729334	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11729695	0.82[EUR][1000 genomes]
rs11729776	0.82[EUR][1000 genomes]
rs11729810	0.82[EUR][1000 genomes]
rs11730695	0.80[EUR][1000 genomes]
rs11730696	0.80[EUR][1000 genomes]
rs11735958	0.80[EUR][1000 genomes]
rs11736405	0.82[EUR][1000 genomes]
rs11736825	0.82[EUR][1000 genomes]
rs11932708	0.82[EUR][1000 genomes]
rs11938734	0.82[EUR][1000 genomes]
rs11938770	0.82[EUR][1000 genomes]
rs11947701	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1465919	0.82[EUR][1000 genomes]
rs1465920	0.82[EUR][1000 genomes]
rs1465921	0.82[EUR][1000 genomes]
rs17001531	0.82[EUR][1000 genomes]
rs17001532	0.82[EUR][1000 genomes]
rs17001533	0.82[EUR][1000 genomes]
rs17001562	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17001584	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17001594	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17001603	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17001622	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17001640	0.99[EUR][1000 genomes]
rs1965813	0.82[EUR][1000 genomes]
rs2289512	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2289513	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28479255	0.82[EUR][1000 genomes]
rs34153791	0.80[EUR][1000 genomes]
rs35369082	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3733257	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3733258	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3733259	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3796496	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3806728	0.84[EUR][1000 genomes]
rs3806729	0.84[EUR][1000 genomes]
rs3806731	0.84[EUR][1000 genomes]
rs3806732	0.81[EUR][1000 genomes]
rs3806733	0.84[EUR][1000 genomes]
rs3821981	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3821982	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs41284767	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4267762	0.82[EUR][1000 genomes]
rs4481255	0.82[EUR][1000 genomes]
rs4597859	0.80[EUR][1000 genomes]
rs4604075	0.82[EUR][1000 genomes]
rs55917550	0.82[EUR][1000 genomes]
rs56085800	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56136722	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56247019	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56923677	0.82[EUR][1000 genomes]
rs56985043	0.82[EUR][1000 genomes]
rs56986239	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs57313943	0.82[EUR][1000 genomes]
rs57317548	0.82[EUR][1000 genomes]
rs57374265	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs57765272	0.82[EUR][1000 genomes]
rs57928417	0.84[EUR][1000 genomes]
rs58036109	0.82[EUR][1000 genomes]
rs58247315	0.82[EUR][1000 genomes]
rs58305323	0.80[EUR][1000 genomes]
rs58528289	0.82[EUR][1000 genomes]
rs58695482	0.82[EUR][1000 genomes]
rs58728245	0.82[EUR][1000 genomes]
rs58822235	0.84[EUR][1000 genomes]
rs58911257	0.82[EUR][1000 genomes]
rs58943792	0.81[EUR][1000 genomes]
rs59084193	0.82[EUR][1000 genomes]
rs59105778	0.82[EUR][1000 genomes]
rs59786688	0.84[EUR][1000 genomes]
rs59847929	0.82[EUR][1000 genomes]
rs59927725	0.82[EUR][1000 genomes]
rs60015167	0.82[EUR][1000 genomes]
rs60017148	0.82[EUR][1000 genomes]
rs60157651	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs60455690	0.82[EUR][1000 genomes]
rs60523248	0.82[EUR][1000 genomes]
rs60671651	0.83[EUR][1000 genomes]
rs60675531	0.82[EUR][1000 genomes]
rs60913446	0.82[EUR][1000 genomes]
rs61102074	0.81[EUR][1000 genomes]
rs61123262	0.84[EUR][1000 genomes]
rs61262669	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61294914	0.82[EUR][1000 genomes]
rs61360019	0.82[EUR][1000 genomes]
rs61598131	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61662067	0.82[EUR][1000 genomes]
rs62300565	0.82[EUR][1000 genomes]
rs62300570	0.82[EUR][1000 genomes]
rs62300572	0.82[EUR][1000 genomes]
rs62300573	0.82[EUR][1000 genomes]
rs62300609	0.82[EUR][1000 genomes]
rs62300610	0.82[EUR][1000 genomes]
rs62300611	0.82[EUR][1000 genomes]
rs62300615	0.82[EUR][1000 genomes]
rs62300617	0.80[EUR][1000 genomes]
rs62300618	0.82[EUR][1000 genomes]
rs62300619	0.82[EUR][1000 genomes]
rs62300620	0.82[EUR][1000 genomes]
rs62300621	0.82[EUR][1000 genomes]
rs62300624	0.82[EUR][1000 genomes]
rs62300625	0.82[EUR][1000 genomes]
rs62300626	0.82[EUR][1000 genomes]
rs62300627	0.82[EUR][1000 genomes]
rs62300628	0.82[EUR][1000 genomes]
rs62300629	0.82[EUR][1000 genomes]
rs62300630	0.80[EUR][1000 genomes]
rs62300633	0.82[EUR][1000 genomes]
rs62300636	0.82[EUR][1000 genomes]
rs62302566	0.82[EUR][1000 genomes]
rs62302649	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62302654	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62302656	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62302659	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6532225	0.84[EUR][1000 genomes]
rs6532226	0.84[EUR][1000 genomes]
rs6532227	0.84[EUR][1000 genomes]
rs6532229	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6532232	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6811781	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6813486	0.82[EUR][1000 genomes]
rs6823680	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6824251	0.82[EUR][1000 genomes]
rs6824981	0.82[EUR][1000 genomes]
rs6841815	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6846685	0.82[EUR][1000 genomes]
rs6846711	0.84[EUR][1000 genomes]
rs6847897	0.81[EUR][1000 genomes]
rs6848297	0.82[EUR][1000 genomes]
rs6852859	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6856063	0.82[EUR][1000 genomes]
rs6856325	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6856933	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6857806	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs747908	0.82[EUR][1000 genomes]
rs747909	0.82[EUR][1000 genomes]
rs7667681	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7667810	0.82[EUR][1000 genomes]
rs7668038	0.82[EUR][1000 genomes]
rs7668869	0.84[EUR][1000 genomes]
rs7674984	0.82[EUR][1000 genomes]
rs7675428	0.82[EUR][1000 genomes]
rs7676834	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7677231	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7679797	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7686870	0.80[EUR][1000 genomes]
rs7688452	0.82[EUR][1000 genomes]
rs7692202	0.81[EUR][1000 genomes]
rs7696379	0.84[EUR][1000 genomes]
rs7698392	0.82[EUR][1000 genomes]
rs8475	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs894246	0.85[EUR][1000 genomes]
rs894251	0.81[EUR][1000 genomes]
rs9917853	0.82[EUR][1000 genomes]
rs9917948	0.82[EUR][1000 genomes]
rs9918072	0.82[EUR][1000 genomes]
rs999357	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs999360	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[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	nsv461558	chr4:77033725-77115553	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	nsv594694	chr4:77033725-77115553	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs62302961	NUP54	cis	Nerve Tibial	GTEx
rs62302961	NUP54	cis	Thyroid	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:77070600-77113600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr4:77071200-77113600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr4:77080600-77113600	Weak transcription	Thymus	Thymus
4	chr4:77090000-77113600	Weak transcription	A549	lung
5	chr4:77090200-77114800	Weak transcription	Hela-S3	cervix
6	chr4:77091000-77114200	Weak transcription	HMEC	breast
7	chr4:77094400-77113800	Weak transcription	Fetal Thymus	thymus
8	chr4:77096800-77114000	Weak transcription	Small Intestine	intestine
9	chr4:77097200-77113600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr4:77097400-77115000	Weak transcription	NH-A	brain
11	chr4:77097600-77119600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
12	chr4:77101400-77114200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr4:77104600-77113800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr4:77105600-77115000	Weak transcription	Fetal Heart	heart
15	chr4:77107800-77113600	Weak transcription	HepG2	liver
16	chr4:77107800-77114000	Weak transcription	HUVEC	blood vessel
17	chr4:77107800-77114200	Weak transcription	Right Atrium	heart
18	chr4:77107800-77114800	Weak transcription	Colonic Mucosa	Colon
19	chr4:77109600-77113600	Strong transcription	Monocytes-CD14+_RO01746	blood
20	chr4:77109600-77113800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr4:77109800-77117400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
22	chr4:77110000-77114200	Strong transcription	Fetal Muscle Trunk	muscle
23	chr4:77110200-77113600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr4:77110200-77113800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr4:77110200-77114200	Weak transcription	Right Ventricle	heart
26	chr4:77110200-77114400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr4:77110200-77117000	Strong transcription	Primary T cells from cord blood	blood
28	chr4:77110400-77113600	Strong transcription	Fetal Stomach	stomach
29	chr4:77110400-77114600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr4:77110600-77116600	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr4:77111000-77118000	Strong transcription	Duodenum Mucosa	Duodenum
32	chr4:77111200-77115200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr4:77111400-77114400	Strong transcription	Placenta	Placenta
34	chr4:77111400-77115000	Strong transcription	Muscle Satellite Cultured Cells	--
35	chr4:77111600-77114200	Weak transcription	Psoas Muscle	Psoas
36	chr4:77111600-77114600	Strong transcription	Osteobl	bone
37	chr4:77112000-77114600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr4:77112000-77115000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr4:77112200-77113600	Strong transcription	Primary T helper cells fromperipheralblood	blood
40	chr4:77112200-77113600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr4:77112200-77114800	Strong transcription	NHLF	lung
42	chr4:77112400-77114000	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr4:77112400-77114000	Strong transcription	Brain Hippocampus Middle	brain
44	chr4:77112400-77114400	ZNF genes & repeats	Primary hematopoietic stem cells	blood
45	chr4:77112400-77114400	ZNF genes & repeats	Brain Germinal Matrix	brain
46	chr4:77112400-77114600	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr4:77112400-77114600	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
48	chr4:77112400-77114600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr4:77112400-77114800	Genic enhancers	Brain Dorsolateral Prefrontal Cortex	brain
50	chr4:77112400-77115200	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood

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