Variant report

Variant	rs11725489
Chromosome Location	chr4:77075794-77075795
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:77067214..77072530-chr4:77074887..77081962,12	K562	blood:
2	chr4:77068526..77071865-chr4:77074983..77079477,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000138750	Chromatin interaction

Extended variants
information (count: 145 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:135)

rs_ID	r²[population]
rs11097244	0.91[EUR][1000 genomes]
rs11558468	0.91[EUR][1000 genomes]
rs11558469	0.91[EUR][1000 genomes]
rs11722957	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11724260	0.91[EUR][1000 genomes]
rs11724543	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11725016	0.91[EUR][1000 genomes]
rs11727718	0.91[EUR][1000 genomes]
rs11729695	0.91[EUR][1000 genomes]
rs11729776	0.91[EUR][1000 genomes]
rs11729810	0.91[EUR][1000 genomes]
rs11729816	0.83[EUR][1000 genomes]
rs11730695	0.89[EUR][1000 genomes]
rs11730696	0.89[EUR][1000 genomes]
rs11735958	0.91[EUR][1000 genomes]
rs11736405	0.91[EUR][1000 genomes]
rs11736825	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11932708	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11938734	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11938770	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1465919	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1465920	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1465921	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17001531	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17001532	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17001533	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1965813	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs28479255	0.91[EUR][1000 genomes]
rs34153791	0.89[EUR][1000 genomes]
rs34384134	0.84[EUR][1000 genomes]
rs35040945	0.88[EUR][1000 genomes]
rs35672178	0.90[EUR][1000 genomes]
rs3806728	0.91[EUR][1000 genomes]
rs3806729	0.91[EUR][1000 genomes]
rs3806731	0.91[EUR][1000 genomes]
rs3806732	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3806733	0.91[EUR][1000 genomes]
rs4267762	0.91[EUR][1000 genomes]
rs4478213	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4481255	0.91[EUR][1000 genomes]
rs4597859	0.89[EUR][1000 genomes]
rs4604075	0.91[EUR][1000 genomes]
rs55917550	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs56923677	0.91[EUR][1000 genomes]
rs56985043	0.91[EUR][1000 genomes]
rs57313943	0.91[EUR][1000 genomes]
rs57317548	0.91[EUR][1000 genomes]
rs57765272	0.91[EUR][1000 genomes]
rs57928417	0.91[EUR][1000 genomes]
rs58036109	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs58247315	0.91[EUR][1000 genomes]
rs58305323	0.89[EUR][1000 genomes]
rs58528289	0.91[EUR][1000 genomes]
rs58695482	0.91[EUR][1000 genomes]
rs58728245	0.91[EUR][1000 genomes]
rs58822235	0.91[EUR][1000 genomes]
rs58911257	0.91[EUR][1000 genomes]
rs58943792	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs59084193	0.91[EUR][1000 genomes]
rs59105778	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs59786688	0.91[EUR][1000 genomes]
rs59847929	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs59850201	0.86[EUR][1000 genomes]
rs59927725	0.91[EUR][1000 genomes]
rs60015167	0.91[EUR][1000 genomes]
rs60017148	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs60455690	0.91[EUR][1000 genomes]
rs60523248	0.91[EUR][1000 genomes]
rs60671651	0.90[EUR][1000 genomes]
rs60675531	0.91[EUR][1000 genomes]
rs60913446	0.91[EUR][1000 genomes]
rs61102074	0.90[EUR][1000 genomes]
rs61123262	0.91[EUR][1000 genomes]
rs61294914	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs61360019	0.91[EUR][1000 genomes]
rs61662067	0.91[EUR][1000 genomes]
rs62300565	0.91[EUR][1000 genomes]
rs62300570	0.91[EUR][1000 genomes]
rs62300572	0.91[EUR][1000 genomes]
rs62300573	0.91[EUR][1000 genomes]
rs62300609	0.91[EUR][1000 genomes]
rs62300610	0.91[EUR][1000 genomes]
rs62300611	0.91[EUR][1000 genomes]
rs62300615	0.91[EUR][1000 genomes]
rs62300616	0.85[EUR][1000 genomes]
rs62300617	0.89[EUR][1000 genomes]
rs62300618	0.91[EUR][1000 genomes]
rs62300619	0.91[EUR][1000 genomes]
rs62300620	0.91[EUR][1000 genomes]
rs62300621	0.91[EUR][1000 genomes]
rs62300624	0.91[EUR][1000 genomes]
rs62300625	0.91[EUR][1000 genomes]
rs62300626	0.91[EUR][1000 genomes]
rs62300627	0.91[EUR][1000 genomes]
rs62300628	0.91[EUR][1000 genomes]
rs62300629	0.91[EUR][1000 genomes]
rs62300630	0.89[EUR][1000 genomes]
rs62300633	0.91[EUR][1000 genomes]
rs62300636	0.91[EUR][1000 genomes]
rs62302566	0.91[EUR][1000 genomes]
rs6532225	0.91[EUR][1000 genomes]
rs6532226	0.91[EUR][1000 genomes]
rs6532227	0.91[EUR][1000 genomes]
rs6813486	0.91[EUR][1000 genomes]
rs6824251	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6824981	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6836703	0.81[ASN][1000 genomes]
rs6838328	0.81[ASN][1000 genomes]
rs6843361	0.81[ASN][1000 genomes]
rs6846685	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6846711	0.91[EUR][1000 genomes]
rs6847897	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6848297	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6856063	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs747908	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs747909	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7666779	0.98[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7667810	0.91[EUR][1000 genomes]
rs7668038	0.91[EUR][1000 genomes]
rs7668869	0.91[EUR][1000 genomes]
rs7674984	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7675428	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7686854	0.90[EUR][1000 genomes]
rs7686870	0.89[EUR][1000 genomes]
rs7688452	0.91[EUR][1000 genomes]
rs7692202	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7696379	0.91[EUR][1000 genomes]
rs7697580	0.88[EUR][1000 genomes]
rs7697777	0.87[EUR][1000 genomes]
rs7698392	0.91[EUR][1000 genomes]
rs894245	0.84[EUR][1000 genomes]
rs894246	0.90[EUR][1000 genomes]
rs9917853	0.91[EUR][1000 genomes]
rs9917948	0.91[EUR][1000 genomes]
rs9918072	0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 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
3	nsv470047	chr4:77033590-77096777	Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
4	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
5	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
6	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
7	nsv1008318	chr4:77042356-77095658	Flanking Active TSS Active TSS Strong transcription Weak transcription Genic enhancers 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	18 gene(s)	inside rSNPs	diseases
8	nsv537144	chr4:77042356-77095658	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
9	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
10	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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11725489	NUP54	cis	Thyroid	GTEx
rs11725489	NUP54	cis	Nerve Tibial	GTEx
rs11725489	NUP54	cis	Esophagus Muscularis	GTEx

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:77070000-77082600	Weak transcription	Spleen	Spleen
2	chr4:77070200-77081000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
3	chr4:77070200-77082200	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr4:77070200-77082400	Weak transcription	Small Intestine	intestine
5	chr4:77070200-77082600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr4:77070200-77082600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr4:77070200-77082600	Weak transcription	Gastric	stomach
8	chr4:77070200-77082800	Weak transcription	Lung	lung
9	chr4:77070400-77077600	Weak transcription	Ovary	ovary
10	chr4:77070400-77079400	Weak transcription	Primary neutrophils fromperipheralblood	blood
11	chr4:77070400-77081600	Weak transcription	Left Ventricle	heart
12	chr4:77070400-77082000	Weak transcription	Primary B cells from cord blood	blood
13	chr4:77070400-77082200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
14	chr4:77070400-77082200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr4:77070400-77082600	Weak transcription	Aorta	Aorta
16	chr4:77070400-77093400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
17	chr4:77070600-77077200	Weak transcription	Primary hematopoietic stem cells	blood
18	chr4:77070600-77078600	Weak transcription	Placenta	Placenta
19	chr4:77070600-77079400	Weak transcription	Fetal Muscle Trunk	muscle
20	chr4:77070600-77079400	Weak transcription	Monocytes-CD14+_RO01746	blood
21	chr4:77070600-77079600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr4:77070600-77079600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr4:77070600-77081400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr4:77070600-77081600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
25	chr4:77070600-77081600	Weak transcription	Primary T helper cells fromperipheralblood	blood
26	chr4:77070600-77082200	Weak transcription	Primary T cells from cord blood	blood
27	chr4:77070600-77082400	Weak transcription	Primary T cells fromperipheralblood	blood
28	chr4:77070600-77083800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
29	chr4:77070600-77113600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
30	chr4:77070800-77077000	Weak transcription	Fetal Stomach	stomach
31	chr4:77070800-77077400	Weak transcription	HSMM	muscle
32	chr4:77070800-77077600	Weak transcription	Brain Anterior Caudate	brain
33	chr4:77070800-77078000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr4:77070800-77079400	Weak transcription	Muscle Satellite Cultured Cells	--
35	chr4:77070800-77079600	Weak transcription	Duodenum Mucosa	Duodenum
36	chr4:77070800-77079600	Weak transcription	Fetal Brain Female	brain
37	chr4:77070800-77079600	Weak transcription	Rectal Mucosa Donor 29	rectum
38	chr4:77070800-77080000	Weak transcription	Stomach Smooth Muscle	stomach
39	chr4:77070800-77080800	Weak transcription	NHDF-Ad	bronchial
40	chr4:77070800-77081400	Weak transcription	HUES6 Cell Line	embryonic stem cell
41	chr4:77070800-77081400	Weak transcription	Rectal Mucosa Donor 31	rectum
42	chr4:77070800-77082000	Weak transcription	HUES48 Cell Line	embryonic stem cell
43	chr4:77070800-77082200	Weak transcription	Fetal Brain Male	brain
44	chr4:77070800-77082400	Weak transcription	NH-A	brain
45	chr4:77070800-77082600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr4:77070800-77082600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
47	chr4:77070800-77082600	Weak transcription	A549	lung
48	chr4:77070800-77083000	Weak transcription	Colonic Mucosa	Colon
49	chr4:77070800-77083800	Weak transcription	Fetal Kidney	kidney
50	chr4:77070800-77088400	Weak transcription	Stomach Mucosa	stomach

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