Variant report

Variant	rs12648687
Chromosome Location	chr4:76879539-76879540
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:76879502..76881277-chr4:76887911..76890255,2	K562	blood:
2	chr4:76879407..76881265-chr4:77068381..77070689,2	K562	blood:

Variant related genes	Relation type
ENSG00000138750	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10337	0.95[ASN][1000 genomes]
rs11726292	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11735706	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12648437	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12651276	1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs17001237	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]
rs17001273	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2271527	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2276885	1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.82[ASN][1000 genomes]
rs2292534	1.00[CEU][hapmap];0.96[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28651740	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2869460	1.00[CHB][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs3733239	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]
rs3796482	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3796483	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4626230	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]
rs57946262	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61281201	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61487959	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs66932304	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs67906710	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs68181445	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6838162	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6840076	0.95[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6841376	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6849878	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7154	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72607852	0.94[ASN][1000 genomes]
rs7654068	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs868007	1.00[YRI][hapmap]

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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12648687	NUP54	cis	Nerve Tibial	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:76862000-76896600	Weak transcription	Stomach Mucosa	stomach
2	chr4:76862200-76886600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr4:76863000-76903600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr4:76863800-76884600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr4:76864600-76884800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr4:76864800-76883800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr4:76864800-76884400	Strong transcription	HUES64 Cell Line	embryonic stem cell
8	chr4:76864800-76884600	Strong transcription	HUES48 Cell Line	embryonic stem cell
9	chr4:76864800-76903000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr4:76866200-76883000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr4:76866400-76886800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr4:76866600-76883000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr4:76867400-76882600	Strong transcription	H1 Cell Line	embryonic stem cell
14	chr4:76867400-76882800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr4:76867400-76883000	Strong transcription	Monocytes-CD14+_RO01746	blood
16	chr4:76867400-76883200	Strong transcription	Osteobl	bone
17	chr4:76867400-76885600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
18	chr4:76867400-76886600	Strong transcription	HUES6 Cell Line	embryonic stem cell
19	chr4:76867800-76882800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
20	chr4:76867800-76883000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr4:76867800-76883200	Strong transcription	Primary monocytes fromperipheralblood	blood
22	chr4:76867800-76883400	Strong transcription	Fetal Muscle Trunk	muscle
23	chr4:76867800-76884600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr4:76867800-76888800	Strong transcription	Liver	Liver
25	chr4:76867800-76900000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr4:76867800-76903800	Strong transcription	Fetal Thymus	thymus
27	chr4:76868000-76882800	Strong transcription	Adipose Nuclei	Adipose
28	chr4:76868000-76882800	Strong transcription	Left Ventricle	heart
29	chr4:76868000-76883000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
30	chr4:76868000-76884600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr4:76868000-76884800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
32	chr4:76868000-76886400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr4:76868000-76886600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
34	chr4:76868000-76899800	Strong transcription	Skeletal Muscle Male	skeletal muscle
35	chr4:76868000-76903000	Strong transcription	Skeletal Muscle Female	skeletal muscle
36	chr4:76868000-76903000	Strong transcription	Stomach Smooth Muscle	stomach
37	chr4:76868000-76903800	Strong transcription	Rectal Mucosa Donor 29	rectum
38	chr4:76868200-76882800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
39	chr4:76868200-76903400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr4:76868200-76903600	Strong transcription	Primary T helper cells fromperipheralblood	blood
41	chr4:76868400-76882800	Strong transcription	Dnd41	blood
42	chr4:76868400-76903600	Strong transcription	Primary T helper cells PMA-I stimulated	--
43	chr4:76868400-76903800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr4:76868400-76903800	Strong transcription	Placenta	Placenta
45	chr4:76869200-76900200	Strong transcription	Duodenum Smooth Muscle	Duodenum
46	chr4:76869800-76882800	Strong transcription	Primary T cells fromperipheralblood	blood
47	chr4:76870000-76886800	Strong transcription	Primary T cells from cord blood	blood
48	chr4:76870600-76882800	Strong transcription	Fetal Intestine Large	intestine
49	chr4:76870600-76883000	Strong transcription	Duodenum Mucosa	Duodenum
50	chr4:76870800-76882800	Strong transcription	Fetal Brain Female	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links