Variant report

Variant	rs4760676
Chromosome Location	chr12:48421663-48421664
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	HNF4A	chr12:48421519-48421734	HepG2	liver:	n/a	n/a
2	FOXA1	chr12:48421398-48421827	HepG2	liver:	n/a	n/a
3	POLR2A	chr12:48421506-48421779	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:48421385..48423662-chr12:48427630..48429692,2	K562	blood:
2	chr12:48420267..48422081-chr12:48425006..48427209,2	K562	blood:
3	chr12:48359708..48361971-chr12:48421078..48422974,2	MCF-7	breast:
4	chr12:48415815..48418237-chr12:48421031..48422834,2	K562	blood:

Variant related genes	Relation type
ENSG00000257955	TF binding region
ENSG00000134291	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10875720	0.93[ASN][1000 genomes]
rs10875722	0.93[ASN][1000 genomes]
rs10875723	0.93[ASN][1000 genomes]
rs10875724	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10875725	0.96[ASN][1000 genomes]
rs10875728	0.82[EUR][1000 genomes]
rs10875729	0.82[EUR][1000 genomes]
rs10875730	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10875731	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10875732	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11168355	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11168357	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11168369	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11168370	0.80[EUR][1000 genomes]
rs11168371	0.96[ASN][1000 genomes]
rs11168374	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12296244	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12305182	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12310999	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1990028	0.91[EUR][1000 genomes]
rs2079295	0.92[ASN][1000 genomes]
rs2269936	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28459711	0.93[ASN][1000 genomes]
rs4760609	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4760610	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61918774	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs719008	0.93[ASN][1000 genomes]
rs7299135	0.93[ASN][1000 genomes]
rs7299271	0.93[ASN][1000 genomes]
rs7299364	0.93[ASN][1000 genomes]
rs7964359	0.83[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832401	chr12:48347453-48477999	Weak transcription Enhancers Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4760676	RP1-228P16.1	cis	Skin Sun Exposed Lower leg	GTEx
rs4760676	RP1-228P16.1	cis	Thyroid	GTEx
rs4760676	RP1-228P16.1	cis	Artery Tibial	GTEx

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:48416800-48423400	Weak transcription	Right Atrium	heart
2	chr12:48417800-48423400	Weak transcription	Fetal Lung	lung
3	chr12:48418000-48422200	Weak transcription	Fetal Heart	heart
4	chr12:48418200-48422200	Weak transcription	Skeletal Muscle Female	skeletal muscle
5	chr12:48418200-48424200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr12:48418400-48425800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr12:48418600-48425200	Enhancers	Fetal Intestine Large	intestine
8	chr12:48419200-48422400	Weak transcription	K562	blood
9	chr12:48420000-48422400	Weak transcription	Colon Smooth Muscle	Colon
10	chr12:48420000-48424200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr12:48420200-48422800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr12:48420200-48423800	Enhancers	Primary hematopoietic stem cells	blood
13	chr12:48420200-48424200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr12:48420400-48421800	Enhancers	Breast Myoepithelial Primary Cells	Breast
15	chr12:48420400-48424000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr12:48420400-48424000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr12:48420400-48424200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr12:48420400-48429000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr12:48420600-48422200	Bivalent Enhancer	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr12:48420600-48424200	Enhancers	Primary hematopoietic stem cells short term culture	blood
21	chr12:48420800-48421800	Bivalent Enhancer	ES-WA7 Cell Line	embryonic stem cell
22	chr12:48420800-48421800	Enhancers	Cortex derived primary cultured neurospheres	brain
23	chr12:48420800-48421800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr12:48420800-48424600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr12:48421000-48421800	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
26	chr12:48421000-48421800	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr12:48421000-48421800	Flanking Active TSS	HepG2	liver
28	chr12:48421000-48422400	Weak transcription	Fetal Kidney	kidney
29	chr12:48421400-48421800	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
30	chr12:48421400-48421800	Enhancers	Rectal Mucosa Donor 31	rectum
31	chr12:48421400-48421800	Enhancers	HMEC	breast
32	chr12:48421400-48422000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr12:48421400-48422800	Enhancers	Placenta Amnion	Placenta Amnion
34	chr12:48421400-48425000	Enhancers	Fetal Intestine Small	intestine
35	chr12:48421600-48421800	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr12:48421600-48422000	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
37	chr12:48421600-48422000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr12:48421600-48423800	Weak transcription	Duodenum Mucosa	Duodenum
39	chr12:48421600-48425000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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