Variant report

Variant	rs999357
Chromosome Location	chr4:77116117-77116118
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	chr17:62221990..62223690-chr4:77114396..77116252,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000199753	Chromatin interaction
ENSG00000266402	Chromatin interaction

Extended variants
information (count: 180 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:180)

rs_ID	r²[population]
rs1051326	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10518144	1.00[CEU][hapmap]
rs10654	1.00[CEU][hapmap]
rs1078350	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11097244	0.82[EUR][1000 genomes]
rs11558468	0.82[EUR][1000 genomes]
rs11558469	0.82[EUR][1000 genomes]
rs11722957	0.90[CEU][hapmap];0.82[EUR][1000 genomes]
rs11724260	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs11725016	0.82[EUR][1000 genomes]
rs11727718	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs11729334	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11729695	0.82[EUR][1000 genomes]
rs11729776	0.82[EUR][1000 genomes]
rs11729810	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs11730695	0.80[EUR][1000 genomes]
rs11730696	0.80[EUR][1000 genomes]
rs11735958	0.80[EUR][1000 genomes]
rs11736405	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs11736825	0.82[EUR][1000 genomes]
rs11932708	0.82[EUR][1000 genomes]
rs11938734	0.82[EUR][1000 genomes]
rs11938770	0.90[CEU][hapmap];0.82[EUR][1000 genomes]
rs11947701	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1465919	0.82[EUR][1000 genomes]
rs1465920	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs1465921	0.82[EUR][1000 genomes]
rs17001390	1.00[CEU][hapmap]
rs17001531	0.82[EUR][1000 genomes]
rs17001532	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs17001533	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs17001562	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17001584	1.00[CEU][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17001594	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17001603	1.00[CEU][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17001622	1.00[CEU][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17001640	1.00[CEU][hapmap];0.99[EUR][1000 genomes]
rs1965813	0.82[EUR][1000 genomes]
rs2289512	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2289513	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28479255	0.82[EUR][1000 genomes]
rs34153791	0.80[EUR][1000 genomes]
rs35369082	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3733257	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3733258	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3733259	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3796496	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3806728	0.84[EUR][1000 genomes]
rs3806729	0.84[EUR][1000 genomes]
rs3806731	0.84[EUR][1000 genomes]
rs3806732	0.81[EUR][1000 genomes]
rs3806733	0.84[EUR][1000 genomes]
rs3821981	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3821982	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs41284767	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs41349449	0.80[CEU][hapmap]
rs41411447	0.80[CEU][hapmap]
rs4267762	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs4308383	0.80[CEU][hapmap]
rs4481255	0.82[EUR][1000 genomes]
rs4597859	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs4604075	0.82[EUR][1000 genomes]
rs55917550	0.82[EUR][1000 genomes]
rs56085800	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56136722	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56247019	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56923677	0.82[EUR][1000 genomes]
rs56985043	0.82[EUR][1000 genomes]
rs56986239	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs57313943	0.82[EUR][1000 genomes]
rs57317548	0.82[EUR][1000 genomes]
rs57374265	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs57765272	0.82[EUR][1000 genomes]
rs57928417	0.84[EUR][1000 genomes]
rs58036109	0.82[EUR][1000 genomes]
rs58247315	0.82[EUR][1000 genomes]
rs58305323	0.80[EUR][1000 genomes]
rs58528289	0.82[EUR][1000 genomes]
rs58695482	0.82[EUR][1000 genomes]
rs58728245	0.82[EUR][1000 genomes]
rs58822235	0.84[EUR][1000 genomes]
rs58911257	0.82[EUR][1000 genomes]
rs58943792	0.81[EUR][1000 genomes]
rs59084193	0.82[EUR][1000 genomes]
rs59105778	0.82[EUR][1000 genomes]
rs59786688	0.84[EUR][1000 genomes]
rs59847929	0.82[EUR][1000 genomes]
rs59927725	0.82[EUR][1000 genomes]
rs60015167	0.82[EUR][1000 genomes]
rs60017148	0.82[EUR][1000 genomes]
rs60157651	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs60455690	0.82[EUR][1000 genomes]
rs60523248	0.82[EUR][1000 genomes]
rs60671651	0.83[EUR][1000 genomes]
rs60675531	0.82[EUR][1000 genomes]
rs60913446	0.82[EUR][1000 genomes]
rs61102074	0.81[EUR][1000 genomes]
rs61123262	0.84[EUR][1000 genomes]
rs61262669	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61294914	0.82[EUR][1000 genomes]
rs61360019	0.82[EUR][1000 genomes]
rs61598131	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61662067	0.82[EUR][1000 genomes]
rs62300565	0.82[EUR][1000 genomes]
rs62300570	0.82[EUR][1000 genomes]
rs62300572	0.82[EUR][1000 genomes]
rs62300573	0.82[EUR][1000 genomes]
rs62300609	0.82[EUR][1000 genomes]
rs62300610	0.82[EUR][1000 genomes]
rs62300611	0.82[EUR][1000 genomes]
rs62300615	0.82[EUR][1000 genomes]
rs62300617	0.80[EUR][1000 genomes]
rs62300618	0.82[EUR][1000 genomes]
rs62300619	0.82[EUR][1000 genomes]
rs62300620	0.82[EUR][1000 genomes]
rs62300621	0.82[EUR][1000 genomes]
rs62300624	0.82[EUR][1000 genomes]
rs62300625	0.82[EUR][1000 genomes]
rs62300626	0.82[EUR][1000 genomes]
rs62300627	0.82[EUR][1000 genomes]
rs62300628	0.82[EUR][1000 genomes]
rs62300629	0.82[EUR][1000 genomes]
rs62300630	0.80[EUR][1000 genomes]
rs62300633	0.82[EUR][1000 genomes]
rs62300636	0.82[EUR][1000 genomes]
rs62302566	0.82[EUR][1000 genomes]
rs62302649	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62302654	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62302656	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62302659	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62302961	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6532201	1.00[CEU][hapmap]
rs6532225	0.84[EUR][1000 genomes]
rs6532226	0.84[EUR][1000 genomes]
rs6532227	0.84[EUR][1000 genomes]
rs6532229	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6532232	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6811781	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6813486	0.82[EUR][1000 genomes]
rs6823680	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6824251	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs6824981	0.82[EUR][1000 genomes]
rs6836703	1.00[CEU][hapmap]
rs6841815	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6846685	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs6846711	0.84[EUR][1000 genomes]
rs6847897	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs6848297	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs6852859	1.00[CEU][hapmap];0.81[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6856063	0.82[EUR][1000 genomes]
rs6856325	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6856933	0.89[CEU][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6857806	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs747908	0.82[EUR][1000 genomes]
rs747909	0.82[EUR][1000 genomes]
rs7657846	1.00[CEU][hapmap]
rs7667681	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7667810	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs7668038	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs7668869	0.84[EUR][1000 genomes]
rs7674984	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs7675107	1.00[CEU][hapmap]
rs7675428	0.82[EUR][1000 genomes]
rs7675618	0.80[CEU][hapmap]
rs7676834	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7677231	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7679611	1.00[CEU][hapmap]
rs7679797	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7686870	0.80[EUR][1000 genomes]
rs7688452	0.82[EUR][1000 genomes]
rs7692202	0.81[EUR][1000 genomes]
rs7696379	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs7698392	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs8475	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs894246	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs894251	0.81[EUR][1000 genomes]
rs9917853	0.82[EUR][1000 genomes]
rs9917948	0.82[EUR][1000 genomes]
rs9918072	0.82[EUR][1000 genomes]
rs999360	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
rs999357	NUP54	cis	Nerve Tibial	GTEx
rs999357	NUP54	cis	Thyroid	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	chr4:77109800-77117400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr4:77110200-77117000	Strong transcription	Primary T cells from cord blood	blood
4	chr4:77110600-77116600	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr4:77111000-77118000	Strong transcription	Duodenum Mucosa	Duodenum
6	chr4:77112400-77117000	Genic enhancers	Brain Substantia Nigra	brain
7	chr4:77112600-77116200	Strong transcription	Rectal Mucosa Donor 29	rectum
8	chr4:77112600-77117000	Strong transcription	Primary neutrophils fromperipheralblood	blood
9	chr4:77113000-77117000	Strong transcription	Rectal Smooth Muscle	rectum
10	chr4:77113000-77117200	Strong transcription	Primary T helper cells PMA-I stimulated	--
11	chr4:77113000-77117400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr4:77113200-77117000	Strong transcription	Primary T cells fromperipheralblood	blood
13	chr4:77113200-77134000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr4:77113400-77116200	Genic enhancers	Brain Angular Gyrus	brain
15	chr4:77113400-77116800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
16	chr4:77113400-77117200	Strong transcription	Stomach Smooth Muscle	stomach
17	chr4:77113600-77116200	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
18	chr4:77113600-77117000	Genic enhancers	Monocytes-CD14+_RO01746	blood
19	chr4:77113600-77118800	Strong transcription	Dnd41	blood
20	chr4:77113600-77134200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
21	chr4:77113800-77116200	Genic enhancers	Brain Cingulate Gyrus	brain
22	chr4:77113800-77116200	Strong transcription	Fetal Brain Male	brain
23	chr4:77113800-77116600	Strong transcription	Primary B cells from peripheral blood	blood
24	chr4:77113800-77116800	Genic enhancers	Brain Anterior Caudate	brain
25	chr4:77113800-77117000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr4:77113800-77118200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr4:77113800-77119400	Weak transcription	H9 Cell Line	embryonic stem cell
28	chr4:77114000-77116800	Genic enhancers	Brain Hippocampus Middle	brain
29	chr4:77114000-77116800	Enhancers	Small Intestine	intestine
30	chr4:77114000-77117000	Strong transcription	HUVEC	blood vessel
31	chr4:77114000-77117400	Genic enhancers	Skeletal Muscle Male	skeletal muscle
32	chr4:77114000-77118800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr4:77114200-77116600	Strong transcription	Cortex derived primary cultured neurospheres	brain
34	chr4:77114200-77117000	Genic enhancers	Brain Inferior Temporal Lobe	brain
35	chr4:77114200-77117000	Strong transcription	Fetal Lung	lung
36	chr4:77114200-77118400	Genic enhancers	Skeletal Muscle Female	skeletal muscle
37	chr4:77114200-77122400	Enhancers	Right Ventricle	heart
38	chr4:77114400-77116200	Weak transcription	HepG2	liver
39	chr4:77114400-77116600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr4:77114400-77116600	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr4:77114400-77116800	Strong transcription	Primary B cells from cord blood	blood
42	chr4:77114400-77116800	Strong transcription	Primary hematopoietic stem cells	blood
43	chr4:77114400-77116800	Strong transcription	Brain Germinal Matrix	brain
44	chr4:77114400-77116800	Strong transcription	Fetal Kidney	kidney
45	chr4:77114400-77117000	Strong transcription	Primary T helper cells fromperipheralblood	blood
46	chr4:77114400-77117000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
47	chr4:77114400-77117000	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
48	chr4:77114400-77117000	Genic enhancers	Placenta	Placenta
49	chr4:77114400-77118200	Enhancers	Stomach Mucosa	stomach
50	chr4:77114400-77118800	Genic enhancers	Fetal Intestine Small	intestine

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