Variant report

Variant	rs3733239
Chromosome Location	chr4:76902775-76902776
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:76902021..76904810-chr4:76904972..76908899,4	MCF-7	breast:

Extended variants
information (count: 32 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs10337	0.96[ASN][1000 genomes]
rs11726292	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11735706	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12648437	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12648687	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12651276	1.00[CHB][hapmap];0.98[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.90[MEX][hapmap];0.85[TSI][hapmap];0.94[ASN][1000 genomes]
rs17001237	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17001273	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2271527	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2276885	1.00[CHB][hapmap];0.98[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.90[MEX][hapmap];0.85[TSI][hapmap];0.82[ASN][1000 genomes]
rs2292534	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28651740	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2869460	1.00[CHB][hapmap];0.95[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.90[MEX][hapmap];0.85[TSI][hapmap];0.91[YRI][hapmap];0.96[ASN][1000 genomes]
rs3796482	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3796483	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4626230	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]
rs57946262	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61281201	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61487959	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs66932304	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs67906710	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs68181445	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6838162	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6840076	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6841376	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6849878	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7154	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72607852	0.94[ASN][1000 genomes]
rs7654068	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][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	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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs3733239	NUP54	cis	parietal	SCAN
rs3733239	SCARB2	cis	parietal	SCAN
rs3733239	NUP54	cis	Nerve Tibial	GTEx
rs3733239	FRAS1	cis	parietal	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:76863000-76903600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
2	chr4:76864800-76903000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr4:76867800-76903800	Strong transcription	Fetal Thymus	thymus
4	chr4:76868000-76903000	Strong transcription	Skeletal Muscle Female	skeletal muscle
5	chr4:76868000-76903000	Strong transcription	Stomach Smooth Muscle	stomach
6	chr4:76868000-76903800	Strong transcription	Rectal Mucosa Donor 29	rectum
7	chr4:76868200-76903400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr4:76868200-76903600	Strong transcription	Primary T helper cells fromperipheralblood	blood
9	chr4:76868400-76903600	Strong transcription	Primary T helper cells PMA-I stimulated	--
10	chr4:76868400-76903800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr4:76868400-76903800	Strong transcription	Placenta	Placenta
12	chr4:76872200-76902800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr4:76883800-76903000	Strong transcription	Duodenum Mucosa	Duodenum
14	chr4:76884000-76902800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr4:76884200-76902800	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr4:76884200-76903800	Strong transcription	Primary T cells fromperipheralblood	blood
17	chr4:76884600-76902800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr4:76884600-76902800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr4:76884600-76902800	Strong transcription	Adipose Nuclei	Adipose
20	chr4:76884600-76903400	Strong transcription	HMEC	breast
21	chr4:76884600-76903400	Strong transcription	HSMM	muscle
22	chr4:76884600-76903600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr4:76884600-76903600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr4:76884600-76903800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
25	chr4:76884800-76903600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
26	chr4:76884800-76903600	Strong transcription	NHEK	skin
27	chr4:76885000-76903000	Strong transcription	Rectal Mucosa Donor 31	rectum
28	chr4:76885200-76903800	Strong transcription	Fetal Intestine Large	intestine
29	chr4:76885400-76903600	Strong transcription	HUES48 Cell Line	embryonic stem cell
30	chr4:76887000-76903800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
31	chr4:76887200-76903400	Strong transcription	Dnd41	blood
32	chr4:76887200-76903600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr4:76887200-76903800	Strong transcription	H9 Cell Line	embryonic stem cell
34	chr4:76887200-76903800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
35	chr4:76887200-76906000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr4:76887200-76911000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
37	chr4:76887600-76903600	Strong transcription	HUES6 Cell Line	embryonic stem cell
38	chr4:76887800-76909600	Weak transcription	Pancreatic Islets	Pancreatic Islet
39	chr4:76889800-76903400	Strong transcription	Liver	Liver
40	chr4:76894200-76910200	Weak transcription	Small Intestine	intestine
41	chr4:76894400-76903600	Strong transcription	GM12878-XiMat	blood
42	chr4:76895000-76903000	Strong transcription	Brain Anterior Caudate	brain
43	chr4:76895400-76910400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
44	chr4:76895800-76910200	Weak transcription	Spleen	Spleen
45	chr4:76896600-76902800	Strong transcription	HSMMtube	muscle
46	chr4:76897600-76910000	Weak transcription	Stomach Mucosa	stomach
47	chr4:76897800-76902800	Strong transcription	H1 Cell Line	embryonic stem cell
48	chr4:76897800-76903200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr4:76898200-76903000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
50	chr4:76898400-76903400	Strong transcription	Primary hematopoietic stem cells	blood

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