Variant report

Variant	rs62302654
Chromosome Location	chr4:77098431-77098432
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	chr4:77067502..77069433-chr4:77097939..77100714,2	K562	blood:
2	chr4:77067933..77070552-chr4:77097939..77099477,2	K562	blood:

Variant related genes	Relation type
ENSG00000138750	Chromatin interaction

Extended variants
information (count: 102 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:96)

rs_ID	r²[population]
rs1051326	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1078350	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11722957	0.83[EUR][1000 genomes]
rs11729334	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11736825	0.83[EUR][1000 genomes]
rs11932708	0.83[EUR][1000 genomes]
rs11938734	0.83[EUR][1000 genomes]
rs11938770	0.83[EUR][1000 genomes]
rs11947701	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1465919	0.83[EUR][1000 genomes]
rs1465920	0.83[EUR][1000 genomes]
rs1465921	0.83[EUR][1000 genomes]
rs17001531	0.83[EUR][1000 genomes]
rs17001532	0.83[EUR][1000 genomes]
rs17001533	0.83[EUR][1000 genomes]
rs17001562	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17001584	0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17001594	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17001603	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17001622	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17001640	0.94[EUR][1000 genomes]
rs1965813	0.83[EUR][1000 genomes]
rs2289512	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2289513	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35369082	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3733257	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3733258	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3733259	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3796496	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3806728	0.81[EUR][1000 genomes]
rs3806729	0.81[EUR][1000 genomes]
rs3806731	0.81[EUR][1000 genomes]
rs3806732	0.82[EUR][1000 genomes]
rs3806733	0.81[EUR][1000 genomes]
rs3821981	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3821982	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs41284767	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs55917550	0.83[EUR][1000 genomes]
rs56085800	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56136722	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56247019	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56986239	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs57374265	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs57390122	0.85[AFR][1000 genomes]
rs57928417	0.81[EUR][1000 genomes]
rs58036109	0.83[EUR][1000 genomes]
rs58652991	0.85[AFR][1000 genomes]
rs58822235	0.81[EUR][1000 genomes]
rs58943792	0.82[EUR][1000 genomes]
rs59105778	0.83[EUR][1000 genomes]
rs59786688	0.81[EUR][1000 genomes]
rs59847929	0.83[EUR][1000 genomes]
rs60017148	0.83[EUR][1000 genomes]
rs60157651	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61123262	0.81[EUR][1000 genomes]
rs61262669	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61294914	0.83[EUR][1000 genomes]
rs61598131	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62302649	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62302656	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62302659	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62302961	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6532225	0.81[EUR][1000 genomes]
rs6532226	0.81[EUR][1000 genomes]
rs6532227	0.81[EUR][1000 genomes]
rs6532229	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6532232	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6811781	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6823680	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6824251	0.83[EUR][1000 genomes]
rs6824981	0.83[EUR][1000 genomes]
rs6841815	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6846685	0.83[EUR][1000 genomes]
rs6846711	0.81[EUR][1000 genomes]
rs6847897	0.82[EUR][1000 genomes]
rs6848297	0.83[EUR][1000 genomes]
rs6852859	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6856063	0.83[EUR][1000 genomes]
rs6856325	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6856933	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6857806	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs747908	0.83[EUR][1000 genomes]
rs747909	0.83[EUR][1000 genomes]
rs7667681	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7668869	0.81[EUR][1000 genomes]
rs7674984	0.83[EUR][1000 genomes]
rs7675428	0.83[EUR][1000 genomes]
rs7676834	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7677231	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7679797	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7692202	0.81[EUR][1000 genomes]
rs7696379	0.81[EUR][1000 genomes]
rs8475	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs894246	0.82[EUR][1000 genomes]
rs999357	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs999360	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv594693	chr4:77033590-77101068	Active TSS Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
2	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
3	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
4	nsv1000539	chr4:77042356-77105492	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
5	nsv1000178	chr4:77053046-77113080	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
6	esv995458	chr4:77093764-77102178	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs62302654	NUP54	cis	Nerve Tibial	GTEx
rs62302654	NUP54	cis	Thyroid	GTEx

Chromatin state (count:122 , 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	chr4:77078200-77100600	Weak transcription	K562	blood
4	chr4:77078600-77100800	Strong transcription	Placenta	Placenta
5	chr4:77079200-77100800	Strong transcription	Liver	Liver
6	chr4:77079400-77098800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr4:77079400-77100000	Strong transcription	Primary neutrophils fromperipheralblood	blood
8	chr4:77079400-77100800	Strong transcription	Fetal Intestine Large	intestine
9	chr4:77079400-77101400	Strong transcription	Fetal Muscle Trunk	muscle
10	chr4:77079400-77108200	Strong transcription	Monocytes-CD14+_RO01746	blood
11	chr4:77079600-77098800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr4:77079600-77099000	Strong transcription	Rectal Mucosa Donor 29	rectum
13	chr4:77079600-77101200	Strong transcription	Duodenum Mucosa	Duodenum
14	chr4:77079600-77101400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr4:77079800-77101000	Strong transcription	Primary monocytes fromperipheralblood	blood
16	chr4:77080600-77113600	Weak transcription	Thymus	Thymus
17	chr4:77080800-77099000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr4:77080800-77101200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr4:77080800-77101200	Strong transcription	NHDF-Ad	bronchial
20	chr4:77081400-77099200	Strong transcription	Rectal Mucosa Donor 31	rectum
21	chr4:77082400-77101400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr4:77082600-77100800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr4:77083200-77112600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr4:77087000-77101400	Strong transcription	Fetal Lung	lung
25	chr4:77087400-77098800	Strong transcription	HSMM	muscle
26	chr4:77088200-77101400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
27	chr4:77090000-77113600	Weak transcription	A549	lung
28	chr4:77090200-77098600	Weak transcription	Pancreatic Islets	Pancreatic Islet
29	chr4:77090200-77100600	Weak transcription	Stomach Mucosa	stomach
30	chr4:77090200-77113000	Weak transcription	H9 Cell Line	embryonic stem cell
31	chr4:77090200-77114800	Weak transcription	Hela-S3	cervix
32	chr4:77090400-77100800	Weak transcription	Fetal Heart	heart
33	chr4:77090400-77107000	Weak transcription	Aorta	Aorta
34	chr4:77091000-77100800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr4:77091000-77114200	Weak transcription	HMEC	breast
36	chr4:77092000-77100200	Strong transcription	Duodenum Smooth Muscle	Duodenum
37	chr4:77092000-77101000	Strong transcription	Primary T cells from cord blood	blood
38	chr4:77092600-77101000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr4:77093400-77100800	Strong transcription	Primary B cells from cord blood	blood
40	chr4:77094400-77113800	Weak transcription	Fetal Thymus	thymus
41	chr4:77095000-77113400	Weak transcription	Placenta Amnion	Placenta Amnion
42	chr4:77095400-77101200	Weak transcription	H1 Cell Line	embryonic stem cell
43	chr4:77095400-77107000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr4:77095600-77099800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr4:77095600-77103600	Weak transcription	NHEK	skin
46	chr4:77095800-77107000	Weak transcription	Esophagus	oesophagus
47	chr4:77096000-77100600	Weak transcription	Colon Smooth Muscle	Colon
48	chr4:77096200-77099600	Weak transcription	Fetal Intestine Small	intestine
49	chr4:77096200-77099600	Weak transcription	Fetal Stomach	stomach
50	chr4:77096200-77107000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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