Variant report

Variant	rs17001640
Chromosome Location	chr4:77124745-77124746
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:77122932..77125835-chr4:77128901..77130952,2	MCF-7	breast:
2	chr4:77122331..77124750-chr4:77227129..77228896,2	MCF-7	breast:
3	chr4:77117716..77120024-chr4:77122804..77125775,4	K562	blood:
4	chr4:77115676..77118604-chr4:77122425..77126369,3	MCF-7	breast:
5	chr4:77122190..77124913-chr4:77147273..77149332,2	K562	blood:
6	chr4:77122262..77124788-chr4:77127198..77129570,2	K562	blood:

Variant related genes	Relation type
ENSG00000118804	Chromatin interaction
ENSG00000138760	Chromatin interaction

Extended variants
information (count: 184 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:183)

rs_ID	r²[population]
rs1051326	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs10518144	1.00[CEU][hapmap]
rs10654	1.00[CEU][hapmap]
rs1078350	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs11097244	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11558468	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11558469	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11722957	0.91[CEU][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11724260	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11725016	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11727718	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs11729334	0.99[EUR][1000 genomes]
rs11729695	0.81[EUR][1000 genomes]
rs11729776	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11729810	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11730695	0.84[AMR][1000 genomes]
rs11730696	0.84[AMR][1000 genomes]
rs11736405	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11736825	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11932708	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11938734	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11938770	0.91[CEU][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11947701	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs1465919	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1465920	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1465921	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs17001390	1.00[CEU][hapmap]
rs17001531	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs17001532	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs17001533	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs17001562	0.97[EUR][1000 genomes]
rs17001584	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs17001594	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs17001603	1.00[CEU][hapmap];0.99[EUR][1000 genomes]
rs17001622	1.00[CEU][hapmap];0.99[EUR][1000 genomes]
rs1965813	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2289512	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs2289513	0.97[EUR][1000 genomes]
rs28479255	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs34153791	0.84[AMR][1000 genomes]
rs35040945	0.84[AMR][1000 genomes]
rs35369082	0.98[EUR][1000 genomes]
rs3733257	0.97[EUR][1000 genomes]
rs3733258	0.97[EUR][1000 genomes]
rs3733259	1.00[CEU][hapmap];0.99[EUR][1000 genomes]
rs3796496	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs3806728	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3806729	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3806731	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3806732	0.80[EUR][1000 genomes]
rs3806733	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3821981	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs3821982	0.97[EUR][1000 genomes]
rs41284767	0.97[EUR][1000 genomes]
rs41349449	0.81[CEU][hapmap]
rs41411447	0.81[CEU][hapmap]
rs41498548	0.81[CEU][hapmap]
rs4267762	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4308383	0.82[CEU][hapmap]
rs4478213	0.82[AMR][1000 genomes]
rs4481255	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4597859	1.00[CEU][hapmap];0.84[AMR][1000 genomes]
rs4604075	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs55917550	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs56085800	0.90[EUR][1000 genomes]
rs56136722	0.98[EUR][1000 genomes]
rs56247019	0.97[EUR][1000 genomes]
rs56923677	0.81[EUR][1000 genomes]
rs56985043	0.81[EUR][1000 genomes]
rs56986239	0.97[EUR][1000 genomes]
rs57313943	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs57317548	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs57374265	0.99[EUR][1000 genomes]
rs57765272	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs57928417	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs58036109	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs58247315	0.81[EUR][1000 genomes]
rs58305323	0.84[AMR][1000 genomes]
rs58528289	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs58695482	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs58728245	0.81[EUR][1000 genomes]
rs58822235	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs58911257	0.81[EUR][1000 genomes]
rs58943792	0.80[EUR][1000 genomes]
rs59084193	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs59105778	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs59786688	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs59847929	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs59850201	0.81[AMR][1000 genomes]
rs59927725	0.81[EUR][1000 genomes]
rs60015167	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs60017148	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs60157651	0.98[EUR][1000 genomes]
rs60455690	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs60523248	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs60671651	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs60675531	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs60913446	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs61102074	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs61123262	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs61262669	0.97[EUR][1000 genomes]
rs61294914	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs61360019	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs61598131	0.97[EUR][1000 genomes]
rs61662067	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62300565	0.81[EUR][1000 genomes]
rs62300570	0.81[EUR][1000 genomes]
rs62300572	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62300573	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62300609	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62300610	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62300611	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62300615	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62300617	0.82[AMR][1000 genomes]
rs62300618	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62300619	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62300620	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62300621	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62300624	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62300625	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62300626	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62300627	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62300628	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62300629	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62300630	0.84[AMR][1000 genomes]
rs62300633	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62300636	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62302566	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62302649	0.95[EUR][1000 genomes]
rs62302654	0.94[EUR][1000 genomes]
rs62302656	0.97[EUR][1000 genomes]
rs62302659	0.99[EUR][1000 genomes]
rs62302961	0.99[EUR][1000 genomes]
rs6532201	1.00[CEU][hapmap]
rs6532225	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6532226	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6532227	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6532229	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs6532232	0.97[EUR][1000 genomes]
rs6811781	0.93[EUR][1000 genomes]
rs6813486	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6823680	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs6824251	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6824981	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6836703	1.00[CEU][hapmap]
rs6841815	0.95[EUR][1000 genomes]
rs6846685	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6846711	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6847897	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs6848297	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6852859	1.00[CEU][hapmap];0.99[EUR][1000 genomes]
rs6856063	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6856325	0.99[EUR][1000 genomes]
rs6856933	0.89[CEU][hapmap];0.97[EUR][1000 genomes]
rs6857806	0.97[EUR][1000 genomes]
rs747908	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs747909	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7657846	1.00[CEU][hapmap]
rs7667681	0.97[EUR][1000 genomes]
rs7667810	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7668038	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7668869	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7674984	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7675107	1.00[CEU][hapmap]
rs7675428	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7675618	0.81[CEU][hapmap]
rs7676834	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs7677231	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs7679611	1.00[CEU][hapmap]
rs7679797	0.98[EUR][1000 genomes]
rs7688452	0.81[EUR][1000 genomes]
rs7692202	0.84[AMR][1000 genomes]
rs7696379	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7697580	0.82[AMR][1000 genomes]
rs7698392	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs8475	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs894246	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs894251	0.82[EUR][1000 genomes]
rs9917853	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9917948	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9918072	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs999357	1.00[CEU][hapmap];0.99[EUR][1000 genomes]
rs999360	0.96[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1799666	chr4:77119942-77129568	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs17001640	NUP54	cis	Thyroid	GTEx
rs17001640	NUP54	cis	Nerve Tibial	GTEx

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:77113200-77134000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr4:77113600-77134200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr4:77117000-77134000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr4:77117200-77129200	Enhancers	Liver	Liver
5	chr4:77117400-77132800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr4:77118800-77125400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr4:77119800-77127600	Enhancers	Pancreatic Islets	Pancreatic Islet
8	chr4:77120000-77130200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr4:77120200-77129400	Enhancers	Brain Substantia Nigra	brain
10	chr4:77120200-77129600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr4:77120400-77124800	Enhancers	Brain Anterior Caudate	brain
12	chr4:77120400-77129200	Weak transcription	NHEK	skin
13	chr4:77120400-77129400	Weak transcription	Hela-S3	cervix
14	chr4:77120400-77129800	Weak transcription	Dnd41	blood
15	chr4:77121000-77128200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr4:77121000-77129600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr4:77121200-77124800	Enhancers	Brain Angular Gyrus	brain
18	chr4:77121200-77127400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr4:77121200-77129400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr4:77121400-77124800	Enhancers	Skeletal Muscle Female	skeletal muscle
21	chr4:77121400-77124800	Weak transcription	Spleen	Spleen
22	chr4:77121400-77128800	Weak transcription	Primary T helper cells fromperipheralblood	blood
23	chr4:77121400-77129200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr4:77121400-77129200	Weak transcription	NH-A	brain
25	chr4:77121400-77129600	Weak transcription	Primary T cells fromperipheralblood	blood
26	chr4:77121400-77129800	Weak transcription	HUES48 Cell Line	embryonic stem cell
27	chr4:77121400-77132800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr4:77121400-77133600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr4:77121400-77134000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr4:77121600-77126000	Enhancers	Colon Smooth Muscle	Colon
31	chr4:77121600-77129600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
32	chr4:77121600-77131000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
33	chr4:77121800-77124800	Enhancers	Skeletal Muscle Male	skeletal muscle
34	chr4:77122000-77127000	Weak transcription	Sigmoid Colon	Sigmoid Colon
35	chr4:77122000-77127200	Weak transcription	Primary T cells from cord blood	blood
36	chr4:77122000-77127600	Weak transcription	HMEC	breast
37	chr4:77122000-77127800	Weak transcription	Aorta	Aorta
38	chr4:77122000-77129400	Weak transcription	Primary T helper cells PMA-I stimulated	--
39	chr4:77122200-77127000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr4:77122200-77127200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr4:77122200-77128800	Weak transcription	HUVEC	blood vessel
42	chr4:77122200-77129000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr4:77122200-77129600	Weak transcription	Primary B cells from peripheral blood	blood
44	chr4:77122200-77130800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
45	chr4:77122400-77124800	Weak transcription	Fetal Stomach	stomach
46	chr4:77122400-77124800	Weak transcription	Pancreas	Pancrea
47	chr4:77122400-77124800	Weak transcription	Rectal Smooth Muscle	rectum
48	chr4:77122400-77124800	Weak transcription	NHLF	lung
49	chr4:77122400-77126200	Weak transcription	Right Atrium	heart
50	chr4:77122400-77126800	Enhancers	Brain Cingulate Gyrus	brain

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