Variant report

Variant	rs17001594
Chromosome Location	chr4:77107562-77107563
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:77068157..77072103-chr4:77105294..77112080,6	K562	blood:
2	chr4:77103626..77106900-chr4:77107437..77109558,3	K562	blood:
3	chr4:77099739..77102113-chr4:77107352..77109592,2	K562	blood:

Variant related genes	Relation type
ENSG00000138750	Chromatin interaction

Extended variants
information (count: 121 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:118)

rs_ID	r²[population]
rs1051326	1.00[CEU][hapmap];0.85[CHB][hapmap];0.85[JPT][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10518144	1.00[CEU][hapmap]
rs10654	1.00[CEU][hapmap]
rs1078350	1.00[CEU][hapmap];0.83[CHB][hapmap];0.86[JPT][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11722957	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs11724260	1.00[CEU][hapmap]
rs11727718	1.00[CEU][hapmap]
rs11729334	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11729810	1.00[CEU][hapmap]
rs11736405	1.00[CEU][hapmap]
rs11736825	0.84[EUR][1000 genomes]
rs11932708	0.84[EUR][1000 genomes]
rs11938734	0.84[EUR][1000 genomes]
rs11938770	0.90[CEU][hapmap];0.84[EUR][1000 genomes]
rs11947701	1.00[CEU][hapmap];0.86[CHB][hapmap];0.85[JPT][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1465919	0.84[EUR][1000 genomes]
rs1465920	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs1465921	0.84[EUR][1000 genomes]
rs17001390	1.00[CEU][hapmap]
rs17001531	0.84[EUR][1000 genomes]
rs17001532	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs17001533	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs17001562	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs17001584	1.00[CEU][hapmap];0.87[CHB][hapmap];0.86[JPT][hapmap];0.97[EUR][1000 genomes]
rs17001603	1.00[CEU][hapmap];0.87[CHB][hapmap];0.86[JPT][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17001622	1.00[CEU][hapmap];0.86[CHB][hapmap];0.85[JPT][hapmap];0.94[EUR][1000 genomes]
rs17001640	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs1965813	0.84[EUR][1000 genomes]
rs2289512	1.00[CEU][hapmap];0.87[CHB][hapmap];0.86[JPT][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2289513	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs35369082	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3733257	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs3733258	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs3733259	1.00[CEU][hapmap];0.81[CHB][hapmap];0.85[JPT][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3796496	1.00[CEU][hapmap];0.86[CHB][hapmap];0.85[JPT][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs3806728	0.81[EUR][1000 genomes]
rs3806729	0.81[EUR][1000 genomes]
rs3806731	0.81[EUR][1000 genomes]
rs3806732	0.85[EUR][1000 genomes]
rs3806733	0.81[EUR][1000 genomes]
rs3821981	1.00[CEU][hapmap];0.86[CHB][hapmap];0.85[JPT][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs3821982	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs41284767	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs41349449	0.80[CEU][hapmap]
rs41411447	0.80[CEU][hapmap]
rs4267762	1.00[CEU][hapmap]
rs4308383	0.80[CEU][hapmap]
rs4478213	0.80[EUR][1000 genomes]
rs4597859	1.00[CEU][hapmap]
rs55917550	0.84[EUR][1000 genomes]
rs56085800	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs56136722	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs56247019	0.97[EUR][1000 genomes]
rs56986239	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs57374265	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs57928417	0.81[EUR][1000 genomes]
rs58036109	0.84[EUR][1000 genomes]
rs58822235	0.81[EUR][1000 genomes]
rs58943792	0.85[EUR][1000 genomes]
rs59105778	0.84[EUR][1000 genomes]
rs59786688	0.81[EUR][1000 genomes]
rs59847929	0.84[EUR][1000 genomes]
rs60017148	0.84[EUR][1000 genomes]
rs60157651	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs60671651	0.80[EUR][1000 genomes]
rs61123262	0.81[EUR][1000 genomes]
rs61262669	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs61294914	0.84[EUR][1000 genomes]
rs61598131	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs62302649	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62302654	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs62302656	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs62302659	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs62302961	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6532201	1.00[CEU][hapmap]
rs6532225	0.81[EUR][1000 genomes]
rs6532226	0.81[EUR][1000 genomes]
rs6532227	0.81[EUR][1000 genomes]
rs6532229	1.00[CEU][hapmap];0.86[CHB][hapmap];0.85[JPT][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6532232	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6811781	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6823680	1.00[CEU][hapmap];0.86[CHB][hapmap];0.85[JPT][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6824251	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs6824981	0.84[EUR][1000 genomes]
rs6836703	1.00[CEU][hapmap]
rs6841815	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6846685	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs6846711	0.81[EUR][1000 genomes]
rs6847897	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs6848297	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs6852859	1.00[CEU][hapmap];0.86[CHB][hapmap];0.86[JPT][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6856063	0.84[EUR][1000 genomes]
rs6856325	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6856933	0.88[CEU][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6857806	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs747908	0.84[EUR][1000 genomes]
rs747909	0.84[EUR][1000 genomes]
rs7657846	1.00[CEU][hapmap]
rs7667681	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7667810	1.00[CEU][hapmap]
rs7668038	1.00[CEU][hapmap]
rs7668869	0.81[EUR][1000 genomes]
rs7674984	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs7675107	1.00[CEU][hapmap]
rs7675428	0.84[EUR][1000 genomes]
rs7675618	0.80[CEU][hapmap]
rs7676834	1.00[CEU][hapmap];0.86[CHB][hapmap];0.85[JPT][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7677231	1.00[CEU][hapmap];0.90[CHB][hapmap];0.86[JPT][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7679611	1.00[CEU][hapmap]
rs7679797	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7692202	0.82[EUR][1000 genomes]
rs7696379	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs7698392	1.00[CEU][hapmap]
rs8475	1.00[CEU][hapmap];0.87[CHB][hapmap];0.86[JPT][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs894246	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs894251	0.82[EUR][1000 genomes]
rs999357	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs999360	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs17001594	NUP54	cis	Nerve Tibial	GTEx
rs17001594	NUP54	cis	Thyroid	GTEx

Chromatin state (count:119 , 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	chr4:77079400-77108200	Strong transcription	Monocytes-CD14+_RO01746	blood
4	chr4:77080600-77113600	Weak transcription	Thymus	Thymus
5	chr4:77083200-77112600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr4:77090000-77113600	Weak transcription	A549	lung
7	chr4:77090200-77113000	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr4:77090200-77114800	Weak transcription	Hela-S3	cervix
9	chr4:77091000-77114200	Weak transcription	HMEC	breast
10	chr4:77094400-77113800	Weak transcription	Fetal Thymus	thymus
11	chr4:77095000-77113400	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr4:77096200-77113200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
13	chr4:77096200-77113400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
14	chr4:77096800-77114000	Weak transcription	Small Intestine	intestine
15	chr4:77097000-77113200	Weak transcription	HUES48 Cell Line	embryonic stem cell
16	chr4:77097000-77113200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
17	chr4:77097000-77113200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
18	chr4:77097200-77112400	Weak transcription	HUES6 Cell Line	embryonic stem cell
19	chr4:77097200-77113600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr4:77097400-77113400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
21	chr4:77097400-77113400	Weak transcription	Fetal Brain Male	brain
22	chr4:77097400-77115000	Weak transcription	NH-A	brain
23	chr4:77097600-77119600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
24	chr4:77097800-77113400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
25	chr4:77098000-77113000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
26	chr4:77100000-77112600	Weak transcription	HUES64 Cell Line	embryonic stem cell
27	chr4:77100400-77113000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr4:77100800-77112200	Weak transcription	Primary T helper cells fromperipheralblood	blood
29	chr4:77101000-77110200	Weak transcription	Primary T cells from cord blood	blood
30	chr4:77101000-77113400	Weak transcription	Primary B cells from peripheral blood	blood
31	chr4:77101400-77107600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr4:77101400-77109400	Weak transcription	Fetal Lung	lung
33	chr4:77101400-77112200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr4:77101400-77112400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr4:77101400-77113000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
36	chr4:77101400-77113000	Weak transcription	Dnd41	blood
37	chr4:77101400-77113400	Weak transcription	HSMMtube	muscle
38	chr4:77101400-77114200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
39	chr4:77101600-77112400	Weak transcription	Brain Germinal Matrix	brain
40	chr4:77102400-77109200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr4:77103200-77108000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr4:77103600-77108600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr4:77104000-77112400	Weak transcription	NHEK	skin
44	chr4:77104400-77107800	Strong transcription	Fetal Muscle Leg	muscle
45	chr4:77104600-77107800	Weak transcription	Brain Anterior Caudate	brain
46	chr4:77104600-77108600	Strong transcription	Primary B cells from cord blood	blood
47	chr4:77104600-77113800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
48	chr4:77105000-77107800	Strong transcription	Duodenum Mucosa	Duodenum
49	chr4:77105000-77108000	Strong transcription	Primary monocytes fromperipheralblood	blood
50	chr4:77105000-77108600	Strong transcription	HSMM	muscle

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