Variant report

Variant	rs6838328
Chromosome Location	chr4:77030287-77030288
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:76961032..76963158-chr4:77027696..77030643,2	K562	blood:

Variant related genes	Relation type
ENSG00000169248	Chromatin interaction

Extended variants
information (count: 218 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:216)

rs_ID	r²[population]
rs10033843	0.81[AFR][1000 genomes]
rs10518144	0.98[EUR][1000 genomes]
rs10654	0.98[EUR][1000 genomes]
rs11097244	0.84[EUR][1000 genomes]
rs1127695	0.98[EUR][1000 genomes]
rs11558468	0.84[EUR][1000 genomes]
rs11558469	0.84[EUR][1000 genomes]
rs11722957	0.80[EUR][1000 genomes]
rs11724260	0.84[EUR][1000 genomes]
rs11725016	0.84[EUR][1000 genomes]
rs11725358	0.93[EUR][1000 genomes]
rs11725489	0.81[ASN][1000 genomes]
rs11726372	0.98[EUR][1000 genomes]
rs11727718	0.84[EUR][1000 genomes]
rs11729637	0.98[EUR][1000 genomes]
rs11729695	0.84[EUR][1000 genomes]
rs11729776	0.84[EUR][1000 genomes]
rs11729810	0.84[EUR][1000 genomes]
rs11730695	0.82[EUR][1000 genomes]
rs11730696	0.82[EUR][1000 genomes]
rs11733489	0.98[EUR][1000 genomes]
rs11735958	0.82[EUR][1000 genomes]
rs11736405	0.84[EUR][1000 genomes]
rs11736825	0.80[EUR][1000 genomes]
rs11932708	0.80[EUR][1000 genomes]
rs11938734	0.80[EUR][1000 genomes]
rs11938770	0.80[EUR][1000 genomes]
rs1465919	0.80[EUR][1000 genomes]
rs1465920	0.80[EUR][1000 genomes]
rs1465921	0.80[EUR][1000 genomes]
rs14773	0.81[ASN][1000 genomes]
rs17001390	0.98[EUR][1000 genomes]
rs17001422	0.98[EUR][1000 genomes]
rs17001424	0.98[EUR][1000 genomes]
rs17001433	0.98[EUR][1000 genomes]
rs17001531	0.80[EUR][1000 genomes]
rs17001532	0.80[EUR][1000 genomes]
rs17001533	0.80[EUR][1000 genomes]
rs17224545	0.85[EUR][1000 genomes]
rs1965813	0.80[EUR][1000 genomes]
rs28479255	0.84[EUR][1000 genomes]
rs28627281	0.80[ASN][1000 genomes]
rs33997696	0.98[EUR][1000 genomes]
rs34153791	0.82[EUR][1000 genomes]
rs34747816	0.84[EUR][1000 genomes]
rs35040945	0.81[EUR][1000 genomes]
rs35672178	0.81[EUR][1000 genomes]
rs3806728	0.82[EUR][1000 genomes]
rs3806729	0.82[EUR][1000 genomes]
rs3806731	0.82[EUR][1000 genomes]
rs3806732	0.89[ASN][1000 genomes]
rs3806733	0.82[EUR][1000 genomes]
rs41349449	0.84[EUR][1000 genomes]
rs41411447	0.84[EUR][1000 genomes]
rs41498548	0.98[EUR][1000 genomes]
rs4267762	0.84[EUR][1000 genomes]
rs4403073	0.98[EUR][1000 genomes]
rs4408983	0.98[EUR][1000 genomes]
rs4481255	0.84[EUR][1000 genomes]
rs4597859	0.82[EUR][1000 genomes]
rs4604075	0.84[EUR][1000 genomes]
rs4859418	0.83[ASN][1000 genomes]
rs4859610	0.85[ASN][1000 genomes]
rs4859615	0.80[ASN][1000 genomes]
rs55917550	0.80[EUR][1000 genomes]
rs56669417	0.98[EUR][1000 genomes]
rs56670659	0.98[EUR][1000 genomes]
rs56788469	0.98[EUR][1000 genomes]
rs56887664	0.98[EUR][1000 genomes]
rs56923677	0.84[EUR][1000 genomes]
rs56985043	0.84[EUR][1000 genomes]
rs57268096	0.98[EUR][1000 genomes]
rs57313943	0.84[EUR][1000 genomes]
rs57317548	0.84[EUR][1000 genomes]
rs57765272	0.84[EUR][1000 genomes]
rs57928417	0.82[EUR][1000 genomes]
rs57960366	0.98[EUR][1000 genomes]
rs58036109	0.80[EUR][1000 genomes]
rs58127619	0.98[EUR][1000 genomes]
rs58232272	0.91[EUR][1000 genomes]
rs58247315	0.84[EUR][1000 genomes]
rs58305323	0.82[EUR][1000 genomes]
rs58319866	0.98[EUR][1000 genomes]
rs58358710	0.97[EUR][1000 genomes]
rs58380268	0.98[EUR][1000 genomes]
rs58510808	0.94[EUR][1000 genomes]
rs58528289	0.84[EUR][1000 genomes]
rs58695482	0.84[EUR][1000 genomes]
rs58728245	0.84[EUR][1000 genomes]
rs58822235	0.82[EUR][1000 genomes]
rs58911257	0.84[EUR][1000 genomes]
rs58943792	0.89[ASN][1000 genomes]
rs59084193	0.84[EUR][1000 genomes]
rs59105778	0.80[EUR][1000 genomes]
rs59547714	0.98[EUR][1000 genomes]
rs59765882	0.84[EUR][1000 genomes]
rs59786688	0.82[EUR][1000 genomes]
rs59789355	0.98[EUR][1000 genomes]
rs59847929	0.80[EUR][1000 genomes]
rs59927725	0.84[EUR][1000 genomes]
rs60015167	0.84[EUR][1000 genomes]
rs60017148	0.80[EUR][1000 genomes]
rs60160936	0.97[EUR][1000 genomes]
rs60289602	0.91[EUR][1000 genomes]
rs60387070	0.98[EUR][1000 genomes]
rs60455690	0.84[EUR][1000 genomes]
rs60523248	0.84[EUR][1000 genomes]
rs60573877	0.98[EUR][1000 genomes]
rs60610578	0.98[EUR][1000 genomes]
rs60628055	0.86[EUR][1000 genomes]
rs60671651	0.81[EUR][1000 genomes]
rs60675531	0.84[EUR][1000 genomes]
rs60913446	0.84[EUR][1000 genomes]
rs61099048	0.98[EUR][1000 genomes]
rs61102074	0.83[EUR][1000 genomes]
rs61123262	0.82[EUR][1000 genomes]
rs61293119	0.84[EUR][1000 genomes]
rs61294914	0.80[EUR][1000 genomes]
rs61360019	0.84[EUR][1000 genomes]
rs61369069	0.98[EUR][1000 genomes]
rs61391079	0.97[EUR][1000 genomes]
rs61662067	0.84[EUR][1000 genomes]
rs61693363	0.84[EUR][1000 genomes]
rs62299341	0.98[EUR][1000 genomes]
rs62299342	0.98[EUR][1000 genomes]
rs62299348	0.98[EUR][1000 genomes]
rs62299349	0.97[EUR][1000 genomes]
rs62299350	0.97[EUR][1000 genomes]
rs62299352	0.86[EUR][1000 genomes]
rs62299354	0.98[EUR][1000 genomes]
rs62299355	0.98[EUR][1000 genomes]
rs62300565	0.84[EUR][1000 genomes]
rs62300570	0.84[EUR][1000 genomes]
rs62300572	0.84[EUR][1000 genomes]
rs62300573	0.84[EUR][1000 genomes]
rs62300609	0.84[EUR][1000 genomes]
rs62300610	0.84[EUR][1000 genomes]
rs62300611	0.84[EUR][1000 genomes]
rs62300615	0.84[EUR][1000 genomes]
rs62300617	0.82[EUR][1000 genomes]
rs62300618	0.84[EUR][1000 genomes]
rs62300619	0.84[EUR][1000 genomes]
rs62300620	0.84[EUR][1000 genomes]
rs62300621	0.84[EUR][1000 genomes]
rs62300624	0.84[EUR][1000 genomes]
rs62300625	0.84[EUR][1000 genomes]
rs62300626	0.84[EUR][1000 genomes]
rs62300627	0.84[EUR][1000 genomes]
rs62300628	0.84[EUR][1000 genomes]
rs62300629	0.84[EUR][1000 genomes]
rs62300630	0.82[EUR][1000 genomes]
rs62300633	0.84[EUR][1000 genomes]
rs62300636	0.84[EUR][1000 genomes]
rs62302566	0.84[EUR][1000 genomes]
rs62318915	0.91[EUR][1000 genomes]
rs62318924	0.89[EUR][1000 genomes]
rs62318925	0.98[EUR][1000 genomes]
rs62318926	0.98[EUR][1000 genomes]
rs62318928	0.98[EUR][1000 genomes]
rs62318929	0.98[EUR][1000 genomes]
rs6532201	0.98[EUR][1000 genomes]
rs6532225	0.82[EUR][1000 genomes]
rs6532226	0.82[EUR][1000 genomes]
rs6532227	0.82[EUR][1000 genomes]
rs6813486	0.84[EUR][1000 genomes]
rs6813732	0.98[EUR][1000 genomes]
rs6824251	0.80[EUR][1000 genomes]
rs6824981	0.80[EUR][1000 genomes]
rs6836703	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6836715	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6838303	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6840007	0.98[EUR][1000 genomes]
rs6843361	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6846685	0.80[EUR][1000 genomes]
rs6846711	0.82[EUR][1000 genomes]
rs6847897	0.87[ASN][1000 genomes]
rs6848297	0.80[EUR][1000 genomes]
rs6856063	0.80[EUR][1000 genomes]
rs747908	0.80[EUR][1000 genomes]
rs747909	0.80[EUR][1000 genomes]
rs7656282	0.84[EUR][1000 genomes]
rs7656734	0.86[EUR][1000 genomes]
rs7657846	0.98[EUR][1000 genomes]
rs7661431	0.84[EUR][1000 genomes]
rs7662240	0.84[EUR][1000 genomes]
rs7664821	0.98[EUR][1000 genomes]
rs7666779	0.84[ASN][1000 genomes]
rs7666848	0.98[EUR][1000 genomes]
rs7667810	0.84[EUR][1000 genomes]
rs7668038	0.84[EUR][1000 genomes]
rs7668413	0.90[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs7668507	0.98[EUR][1000 genomes]
rs7668869	0.82[EUR][1000 genomes]
rs7670483	0.91[EUR][1000 genomes]
rs7674984	0.80[EUR][1000 genomes]
rs7675107	0.98[EUR][1000 genomes]
rs7675428	0.80[EUR][1000 genomes]
rs7675618	0.91[EUR][1000 genomes]
rs7678836	0.92[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs7679084	0.84[EUR][1000 genomes]
rs7679283	0.84[EUR][1000 genomes]
rs7679611	0.98[EUR][1000 genomes]
rs7686854	0.81[EUR][1000 genomes]
rs7686870	0.82[EUR][1000 genomes]
rs7688452	0.84[EUR][1000 genomes]
rs7690763	0.98[EUR][1000 genomes]
rs7692789	0.95[EUR][1000 genomes]
rs7693762	0.98[EUR][1000 genomes]
rs7695601	0.98[EUR][1000 genomes]
rs7696379	0.82[EUR][1000 genomes]
rs7697701	0.98[EUR][1000 genomes]
rs7698392	0.84[EUR][1000 genomes]
rs894246	0.81[EUR][1000 genomes]
rs9917853	0.84[EUR][1000 genomes]
rs9917948	0.84[EUR][1000 genomes]
rs9918072	0.84[EUR][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	nsv529613	chr4:76654941-77081576	Flanking Active TSS Weak transcription Genic enhancers Strong transcription Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
2	nsv1009047	chr4:76989180-77077885	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6838328	NUP54	cis	Nerve Tibial	GTEx
rs6838328	NUP54	cis	Thyroid	GTEx
rs6838328	NUP54	cis	Esophagus Muscularis	GTEx

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:77017000-77034400	Weak transcription	Right Ventricle	heart
2	chr4:77024000-77032200	Weak transcription	Left Ventricle	heart
3	chr4:77026400-77033400	Weak transcription	HSMMtube	muscle
4	chr4:77026600-77033400	Weak transcription	Skeletal Muscle Female	skeletal muscle
5	chr4:77027200-77033000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr4:77027200-77033400	Weak transcription	Skeletal Muscle Male	skeletal muscle
7	chr4:77027200-77034000	Weak transcription	Brain Anterior Caudate	brain
8	chr4:77027200-77034400	Weak transcription	Fetal Muscle Leg	muscle
9	chr4:77027200-77035400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
10	chr4:77027600-77033400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr4:77027600-77034200	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr4:77027600-77034400	Weak transcription	Brain Hippocampus Middle	brain
13	chr4:77027600-77037400	Weak transcription	Brain Substantia Nigra	brain
14	chr4:77027800-77034200	Weak transcription	Cortex derived primary cultured neurospheres	brain
15	chr4:77027800-77034200	Weak transcription	Fetal Brain Female	brain
16	chr4:77027800-77036400	Weak transcription	Brain Angular Gyrus	brain
17	chr4:77027800-77038400	Weak transcription	Fetal Brain Male	brain
18	chr4:77028000-77033200	Weak transcription	HUES64 Cell Line	embryonic stem cell
19	chr4:77028000-77034000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr4:77028000-77037600	Weak transcription	Brain Cingulate Gyrus	brain
21	chr4:77028000-77068600	Weak transcription	Gastric	stomach
22	chr4:77028400-77033200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr4:77028400-77033400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
24	chr4:77028400-77034400	Weak transcription	K562	blood
25	chr4:77029200-77033800	Weak transcription	HUES48 Cell Line	embryonic stem cell
26	chr4:77029600-77033400	Weak transcription	HSMM	muscle
27	chr4:77030000-77033400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr4:77030000-77033400	Weak transcription	Muscle Satellite Cultured Cells	--
29	chr4:77030000-77034400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr4:77030000-77037400	Weak transcription	NHDF-Ad	bronchial

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