Variant report

Variant	rs999360
Chromosome Location	chr4:77117749-77117750
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr4:77117660-77117810	HPAF	blood vessel:	n/a	n/a
2	CTCF	chr4:77117720-77117870	HBMEC	blood vessel:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:77117574..77120210-chr4:77127527..77130330,2	K562	blood:
2	chr4:77117716..77120024-chr4:77122804..77125775,4	K562	blood:

Variant related genes	Relation type
SCARB2	TF binding region

Extended variants
information (count: 153 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:153)

rs_ID	r²[population]
rs1051326	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1078350	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11097244	0.80[EUR][1000 genomes]
rs11558468	0.80[EUR][1000 genomes]
rs11558469	0.80[EUR][1000 genomes]
rs11722957	0.80[EUR][1000 genomes]
rs11724260	0.80[EUR][1000 genomes]
rs11725016	0.80[EUR][1000 genomes]
rs11727718	0.80[EUR][1000 genomes]
rs11729334	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11729695	0.80[EUR][1000 genomes]
rs11729776	0.80[EUR][1000 genomes]
rs11729810	0.80[EUR][1000 genomes]
rs11736405	0.80[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]
rs11947701	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1465919	0.80[EUR][1000 genomes]
rs1465920	0.80[EUR][1000 genomes]
rs1465921	0.80[EUR][1000 genomes]
rs17001531	0.80[EUR][1000 genomes]
rs17001532	0.80[EUR][1000 genomes]
rs17001533	0.80[EUR][1000 genomes]
rs17001562	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17001584	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17001594	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17001603	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17001622	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17001640	0.96[EUR][1000 genomes]
rs1965813	0.80[EUR][1000 genomes]
rs2289512	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2289513	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28479255	0.80[EUR][1000 genomes]
rs35369082	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3733257	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3733258	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3733259	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3796496	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3806728	0.82[EUR][1000 genomes]
rs3806729	0.82[EUR][1000 genomes]
rs3806731	0.82[EUR][1000 genomes]
rs3806733	0.82[EUR][1000 genomes]
rs3821981	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3821982	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs41284767	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4267762	0.80[EUR][1000 genomes]
rs4481255	0.80[EUR][1000 genomes]
rs4604075	0.80[EUR][1000 genomes]
rs55917550	0.80[EUR][1000 genomes]
rs56085800	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56136722	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56247019	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56923677	0.80[EUR][1000 genomes]
rs56985043	0.80[EUR][1000 genomes]
rs56986239	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs57313943	0.80[EUR][1000 genomes]
rs57317548	0.80[EUR][1000 genomes]
rs57374265	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs57765272	0.80[EUR][1000 genomes]
rs57928417	0.82[EUR][1000 genomes]
rs58036109	0.80[EUR][1000 genomes]
rs58247315	0.80[EUR][1000 genomes]
rs58528289	0.80[EUR][1000 genomes]
rs58695482	0.80[EUR][1000 genomes]
rs58728245	0.80[EUR][1000 genomes]
rs58822235	0.82[EUR][1000 genomes]
rs58911257	0.80[EUR][1000 genomes]
rs59084193	0.80[EUR][1000 genomes]
rs59105778	0.80[EUR][1000 genomes]
rs59786688	0.82[EUR][1000 genomes]
rs59847929	0.80[EUR][1000 genomes]
rs59927725	0.80[EUR][1000 genomes]
rs60015167	0.80[EUR][1000 genomes]
rs60017148	0.80[EUR][1000 genomes]
rs60157651	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs60455690	0.80[EUR][1000 genomes]
rs60523248	0.80[EUR][1000 genomes]
rs60671651	0.81[EUR][1000 genomes]
rs60675531	0.80[EUR][1000 genomes]
rs60913446	0.80[EUR][1000 genomes]
rs61123262	0.82[EUR][1000 genomes]
rs61262669	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61294914	0.80[EUR][1000 genomes]
rs61360019	0.80[EUR][1000 genomes]
rs61598131	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61662067	0.80[EUR][1000 genomes]
rs62300565	0.80[EUR][1000 genomes]
rs62300570	0.80[EUR][1000 genomes]
rs62300572	0.80[EUR][1000 genomes]
rs62300573	0.80[EUR][1000 genomes]
rs62300609	0.80[EUR][1000 genomes]
rs62300610	0.80[EUR][1000 genomes]
rs62300611	0.80[EUR][1000 genomes]
rs62300615	0.80[EUR][1000 genomes]
rs62300618	0.80[EUR][1000 genomes]
rs62300619	0.80[EUR][1000 genomes]
rs62300620	0.80[EUR][1000 genomes]
rs62300621	0.80[EUR][1000 genomes]
rs62300624	0.80[EUR][1000 genomes]
rs62300625	0.80[EUR][1000 genomes]
rs62300626	0.80[EUR][1000 genomes]
rs62300627	0.80[EUR][1000 genomes]
rs62300628	0.80[EUR][1000 genomes]
rs62300629	0.80[EUR][1000 genomes]
rs62300633	0.80[EUR][1000 genomes]
rs62300636	0.80[EUR][1000 genomes]
rs62302566	0.80[EUR][1000 genomes]
rs62302649	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62302654	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62302656	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62302659	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62302961	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6532225	0.82[EUR][1000 genomes]
rs6532226	0.82[EUR][1000 genomes]
rs6532227	0.82[EUR][1000 genomes]
rs6532229	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6532232	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6811781	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6813486	0.80[EUR][1000 genomes]
rs6823680	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6824251	0.80[EUR][1000 genomes]
rs6824981	0.80[EUR][1000 genomes]
rs6841815	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6846685	0.80[EUR][1000 genomes]
rs6846711	0.82[EUR][1000 genomes]
rs6848297	0.80[EUR][1000 genomes]
rs6852859	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6856063	0.80[EUR][1000 genomes]
rs6856325	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6856933	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6857806	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs747908	0.80[EUR][1000 genomes]
rs747909	0.80[EUR][1000 genomes]
rs7667681	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7667810	0.80[EUR][1000 genomes]
rs7668038	0.80[EUR][1000 genomes]
rs7668869	0.82[EUR][1000 genomes]
rs7674984	0.80[EUR][1000 genomes]
rs7675428	0.80[EUR][1000 genomes]
rs7676834	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7677231	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7679797	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7688452	0.80[EUR][1000 genomes]
rs7696379	0.82[EUR][1000 genomes]
rs7698392	0.80[EUR][1000 genomes]
rs8475	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs894246	0.83[EUR][1000 genomes]
rs9917853	0.80[EUR][1000 genomes]
rs9917948	0.80[EUR][1000 genomes]
rs9918072	0.80[EUR][1000 genomes]
rs999357	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs999360	NUP54	cis	Thyroid	GTEx
rs999360	NUP54	cis	Nerve Tibial	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:77097600-77119600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
2	chr4:77111000-77118000	Strong transcription	Duodenum Mucosa	Duodenum
3	chr4:77113200-77134000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr4:77113600-77118800	Strong transcription	Dnd41	blood
5	chr4:77113600-77134200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr4:77113800-77118200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr4:77113800-77119400	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr4:77114000-77118800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr4:77114200-77118400	Genic enhancers	Skeletal Muscle Female	skeletal muscle
10	chr4:77114200-77122400	Enhancers	Right Ventricle	heart
11	chr4:77114400-77118200	Enhancers	Stomach Mucosa	stomach
12	chr4:77114400-77118800	Genic enhancers	Fetal Intestine Small	intestine
13	chr4:77114600-77117800	Strong transcription	Fetal Stomach	stomach
14	chr4:77114600-77118400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr4:77114600-77119400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
16	chr4:77114600-77121000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr4:77114600-77122000	Enhancers	HMEC	breast
18	chr4:77114800-77117800	Strong transcription	Fetal Muscle Leg	muscle
19	chr4:77114800-77122800	Enhancers	Psoas Muscle	Psoas
20	chr4:77115000-77118200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr4:77115000-77118800	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr4:77115000-77118800	Genic enhancers	HSMM	muscle
23	chr4:77115200-77118000	Weak transcription	Aorta	Aorta
24	chr4:77115200-77118200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
25	chr4:77115200-77118800	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr4:77115200-77119400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
27	chr4:77115200-77122200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr4:77115400-77118200	Weak transcription	Esophagus	oesophagus
29	chr4:77115400-77119400	Weak transcription	Placenta Amnion	Placenta Amnion
30	chr4:77115400-77119400	Enhancers	NHLF	lung
31	chr4:77115400-77122600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr4:77115600-77119200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
33	chr4:77115600-77119200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr4:77115600-77119400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
35	chr4:77115600-77120800	Enhancers	Adipose Nuclei	Adipose
36	chr4:77115800-77118200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr4:77115800-77119200	Weak transcription	HUES6 Cell Line	embryonic stem cell
38	chr4:77116000-77119200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
39	chr4:77116200-77118000	Genic enhancers	Muscle Satellite Cultured Cells	--
40	chr4:77116200-77118000	Enhancers	Brain Cingulate Gyrus	brain
41	chr4:77116200-77118400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr4:77116200-77118600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
43	chr4:77116200-77118800	Genic enhancers	Rectal Mucosa Donor 29	rectum
44	chr4:77116200-77119000	Weak transcription	K562	blood
45	chr4:77116200-77119600	Enhancers	Brain Angular Gyrus	brain
46	chr4:77116200-77122400	Enhancers	Pancreas	Pancrea
47	chr4:77116200-77122400	Enhancers	Right Atrium	heart
48	chr4:77116400-77118400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr4:77116400-77119200	Weak transcription	H1 Cell Line	embryonic stem cell
50	chr4:77116400-77119400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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