Variant report

Variant	rs4626230
Chromosome Location	chr4:76863652-76863653
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	chr4:76861625..76863720-chr4:76909476..76912300,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000198301	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10337	0.92[ASN][1000 genomes]
rs11726292	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11735706	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12648437	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12648687	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12651276	0.95[CHB][hapmap];0.86[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap];0.81[MEX][hapmap];0.85[TSI][hapmap];0.90[ASN][1000 genomes]
rs17001237	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17001273	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2271527	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];0.98[GIH][hapmap];0.90[JPT][hapmap];0.88[LWK][hapmap];0.90[MEX][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2276885	0.95[CHB][hapmap];0.86[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap];0.81[MEX][hapmap];0.85[TSI][hapmap]
rs2292534	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28651740	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2869460	0.95[CHB][hapmap];0.89[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap];0.81[MEX][hapmap];0.85[TSI][hapmap];0.91[YRI][hapmap];0.92[ASN][1000 genomes]
rs3733239	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3796482	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3796483	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];0.95[GIH][hapmap];0.91[JPT][hapmap];0.89[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs57946262	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61281201	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61487959	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs66932304	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs67906710	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs68181445	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6838162	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6840076	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6841376	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6849878	1.00[CEU][hapmap];0.95[CHB][hapmap];0.89[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.94[TSI][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7154	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72607852	0.90[ASN][1000 genomes]
rs7654068	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3353539	chr4:76530136-76993859	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	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
3	nsv1004627	chr4:76793910-76999584	Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
4	esv3396277	chr4:76861228-76865426	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4626230	NUP54	cis	parietal	SCAN
rs4626230	CXCL6	cis	cerebellum	SCAN
rs4626230	NUP54	cis	Nerve Tibial	GTEx

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:76862000-76868200	Weak transcription	Fetal Lung	lung
2	chr4:76862000-76871600	Weak transcription	Fetal Kidney	kidney
3	chr4:76862000-76875600	Weak transcription	Fetal Heart	heart
4	chr4:76862000-76896600	Weak transcription	Stomach Mucosa	stomach
5	chr4:76862200-76864600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr4:76862200-76867400	Weak transcription	NHDF-Ad	bronchial
7	chr4:76862200-76868000	Weak transcription	GM12878-XiMat	blood
8	chr4:76862200-76868200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
9	chr4:76862200-76871000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr4:76862200-76871000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
11	chr4:76862200-76875200	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr4:76862200-76876400	Weak transcription	Gastric	stomach
13	chr4:76862200-76876600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr4:76862200-76886600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr4:76862400-76864600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr4:76862400-76864600	Weak transcription	HMEC	breast
17	chr4:76862400-76864800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr4:76862400-76864800	Weak transcription	HSMM	muscle
19	chr4:76862400-76867600	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr4:76862400-76867800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr4:76862400-76868000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr4:76862400-76868000	Weak transcription	Lung	lung
23	chr4:76862400-76868000	Weak transcription	HUVEC	blood vessel
24	chr4:76862400-76868400	Weak transcription	Ovary	ovary
25	chr4:76862400-76868400	Weak transcription	HSMMtube	muscle
26	chr4:76862400-76868600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr4:76862400-76873400	Weak transcription	Colon Smooth Muscle	Colon
28	chr4:76862400-76875400	Weak transcription	Spleen	Spleen
29	chr4:76862400-76876600	Weak transcription	Aorta	Aorta
30	chr4:76862400-76876600	Weak transcription	Small Intestine	intestine
31	chr4:76862600-76864400	Weak transcription	NHEK	skin
32	chr4:76862600-76864800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr4:76862600-76864800	Weak transcription	HUES48 Cell Line	embryonic stem cell
34	chr4:76862600-76864800	Weak transcription	HUES6 Cell Line	embryonic stem cell
35	chr4:76862600-76864800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr4:76862600-76864800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr4:76862600-76865200	Enhancers	Primary monocytes fromperipheralblood	blood
38	chr4:76862600-76865200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr4:76862600-76866200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr4:76862600-76867400	Weak transcription	H1 Cell Line	embryonic stem cell
41	chr4:76862600-76867400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
42	chr4:76862600-76867400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
43	chr4:76862600-76867400	Weak transcription	Brain Hippocampus Middle	brain
44	chr4:76862600-76867400	Weak transcription	Fetal Intestine Large	intestine
45	chr4:76862600-76867400	Weak transcription	Osteobl	bone
46	chr4:76862600-76867600	Weak transcription	Thymus	Thymus
47	chr4:76862600-76867800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr4:76862600-76867800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr4:76862600-76867800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
50	chr4:76862600-76867800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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