Variant report

Variant	rs4760609
Chromosome Location	chr12:48415757-48415758
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:48357498..48359897-chr12:48415530..48417456,2	MCF-7	breast:
2	chr12:48415272..48418773-chr12:48419086..48422802,6	MCF-7	breast:
3	chr12:48212416..48215175-chr12:48415223..48418079,4	MCF-7	breast:
4	chr12:48407751..48410923-chr12:48414618..48417182,4	MCF-7	breast:
5	chr12:48292355..48294336-chr12:48414292..48417246,2	MCF-7	breast:
6	chr12:48294511..48296971-chr12:48414193..48417151,2	MCF-7	breast:
7	chr12:48406038..48410831-chr12:48411860..48418424,9	MCF-7	breast:
8	chr12:48391315..48400584-chr12:48411914..48418489,16	MCF-7	breast:
9	chr12:48367607..48371765-chr12:48415495..48417356,3	MCF-7	breast:
10	chr12:48410357..48413530-chr12:48413703..48417962,3	K562	blood:

No data

Variant related genes	Relation type
ENSG00000139219	Chromatin interaction
ENSG00000134291	Chromatin interaction
ENSG00000061273	Chromatin interaction
ENSG00000257955	Chromatin interaction

Extended variants
information (count: 81 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs10082861	0.82[CHB][hapmap];0.92[JPT][hapmap]
rs10219623	0.93[JPT][hapmap]
rs10875720	0.97[ASN][1000 genomes]
rs10875722	0.97[ASN][1000 genomes]
rs10875723	0.96[ASN][1000 genomes]
rs10875724	0.84[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10875725	0.90[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];0.93[JPT][hapmap];0.93[ASN][1000 genomes]
rs10875730	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10875731	0.93[ASN][1000 genomes]
rs10875732	0.94[CHB][hapmap];0.92[JPT][hapmap];0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs10875745	0.88[GIH][hapmap];0.93[JPT][hapmap]
rs10875746	0.92[GIH][hapmap];0.93[JPT][hapmap]
rs10875750	1.00[GIH][hapmap];0.93[JPT][hapmap];0.85[TSI][hapmap]
rs10875767	0.86[JPT][hapmap]
rs10875770	0.86[JPT][hapmap]
rs10875772	0.86[JPT][hapmap]
rs11168355	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11168357	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11168369	0.85[CEU][hapmap];0.94[CHB][hapmap];0.93[JPT][hapmap];0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs11168371	0.95[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.91[MEX][hapmap];0.93[ASN][1000 genomes]
rs11168374	0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs11168403	0.95[CHB][hapmap];0.93[JPT][hapmap]
rs11168413	0.93[JPT][hapmap]
rs11168414	1.00[GIH][hapmap];0.93[JPT][hapmap];0.84[MEX][hapmap];0.85[TSI][hapmap]
rs11168418	1.00[GIH][hapmap];0.93[JPT][hapmap];0.84[MEX][hapmap];0.85[TSI][hapmap]
rs11168420	1.00[GIH][hapmap];0.93[JPT][hapmap];0.85[TSI][hapmap]
rs11168421	0.84[GIH][hapmap];0.93[JPT][hapmap]
rs11168425	0.93[GIH][hapmap];0.93[JPT][hapmap]
rs11168427	1.00[GIH][hapmap];0.93[JPT][hapmap];0.84[MEX][hapmap];0.85[TSI][hapmap]
rs11168433	1.00[GIH][hapmap];0.93[JPT][hapmap];0.84[MEX][hapmap];0.83[TSI][hapmap]
rs11168450	0.93[JPT][hapmap]
rs11168459	0.86[JPT][hapmap]
rs12228854	0.85[TSI][hapmap]
rs12296244	0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs12297470	0.93[GIH][hapmap];0.93[JPT][hapmap];0.84[MEX][hapmap]
rs12301339	0.89[CEU][hapmap]
rs12304476	0.95[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.92[MEX][hapmap];0.85[TSI][hapmap]
rs12305182	1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12305511	0.88[GIH][hapmap];0.93[JPT][hapmap]
rs12306451	0.95[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.92[MEX][hapmap];0.82[TSI][hapmap]
rs12310813	0.93[GIH][hapmap];0.93[JPT][hapmap];0.84[MEX][hapmap]
rs12310999	0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs12312134	0.86[JPT][hapmap]
rs17122666	0.83[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.84[MEX][hapmap];0.85[TSI][hapmap]
rs17122812	0.86[JPT][hapmap]
rs1859445	0.96[GIH][hapmap];0.93[JPT][hapmap];0.84[MEX][hapmap]
rs1990028	0.92[EUR][1000 genomes]
rs2012773	0.93[JPT][hapmap]
rs2079295	0.93[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2107638	0.93[JPT][hapmap]
rs2228500	1.00[GIH][hapmap];0.93[JPT][hapmap];0.83[MEX][hapmap];0.85[TSI][hapmap]
rs2269933	0.89[GIH][hapmap];0.93[JPT][hapmap]
rs2269935	0.84[GIH][hapmap];0.93[JPT][hapmap];0.84[MEX][hapmap];0.85[TSI][hapmap]
rs2269936	0.84[CEU][hapmap];0.95[CHB][hapmap];0.93[JPT][hapmap];0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28459711	0.97[ASN][1000 genomes]
rs3782910	0.95[CHB][hapmap];0.93[JPT][hapmap]
rs4760610	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4760619	0.93[JPT][hapmap]
rs4760622	0.88[GIH][hapmap];0.93[JPT][hapmap]
rs4760676	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4760681	0.96[GIH][hapmap];0.93[JPT][hapmap];0.84[MEX][hapmap];0.85[TSI][hapmap]
rs4760687	0.93[GIH][hapmap];0.93[JPT][hapmap]
rs4760695	0.88[GIH][hapmap];0.93[JPT][hapmap]
rs4760696	0.93[JPT][hapmap]
rs4760697	0.93[JPT][hapmap]
rs61918774	0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs6580659	0.92[JPT][hapmap]
rs7135779	0.92[JPT][hapmap]
rs719008	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs725454	0.83[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.84[MEX][hapmap];0.85[TSI][hapmap]
rs7299135	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs7299271	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs7299364	0.97[ASN][1000 genomes]
rs7299762	0.81[ASN][1000 genomes]
rs7486424	0.93[JPT][hapmap]
rs7964359	0.87[CHB][hapmap];0.88[ASN][1000 genomes]
rs8804	1.00[GIH][hapmap];0.93[JPT][hapmap];0.84[MEX][hapmap];0.85[TSI][hapmap]
rs886588	0.94[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.92[MEX][hapmap];0.85[TSI][hapmap]
rs989144	0.85[CEU][hapmap];0.95[CHB][hapmap];0.93[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 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
2	esv2760677	chr12:48412410-48416967	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Bivalent/Poised TSS	Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	n/a

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs4760609	LMBR1L	cis	cerebellum	SCAN
rs4760609	RP1-228P16.1	cis	Skin Sun Exposed Lower leg	GTEx
rs4760609	RP1-228P16.1	cis	Thyroid	GTEx
rs4760609	PRKAG1	cis	parietal	SCAN
rs4760609	SENP1	cis	parietal	SCAN
rs4760609	RP1-228P16.1	cis	Artery Tibial	GTEx
rs4760609	ASB8	cis	cerebellum	SCAN
rs4760609	LOC255411	cis	cerebellum	SCAN
rs4760609	RP1-228P16.1	cis	Adipose Subcutaneous	GTEx
rs4760609	SENP1	cis	cerebellum	SCAN

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:48412000-48415800	Weak transcription	Duodenum Mucosa	Duodenum
2	chr12:48415000-48416000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr12:48415000-48416000	Flanking Active TSS	Hela-S3	cervix
4	chr12:48415000-48416800	Enhancers	Right Atrium	heart
5	chr12:48415000-48417800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr12:48415000-48417800	Enhancers	Fetal Lung	lung
7	chr12:48415000-48417800	Enhancers	Rectal Mucosa Donor 31	rectum
8	chr12:48415000-48418000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr12:48415000-48418200	Enhancers	Fetal Intestine Large	intestine
10	chr12:48415000-48418200	Enhancers	Fetal Intestine Small	intestine
11	chr12:48415200-48416000	Enhancers	Gastric	stomach
12	chr12:48415200-48416800	Enhancers	Placenta	Placenta
13	chr12:48415200-48418000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr12:48415200-48418200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr12:48415400-48415800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr12:48415400-48417000	Enhancers	Right Ventricle	heart
17	chr12:48415400-48417800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr12:48415400-48417800	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
19	chr12:48415400-48418000	Enhancers	Fetal Heart	heart
20	chr12:48415400-48418000	Enhancers	HepG2	liver
21	chr12:48415600-48415800	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr12:48415600-48415800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr12:48415600-48415800	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
24	chr12:48415600-48415800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr12:48415600-48415800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr12:48415600-48415800	Bivalent Enhancer	Fetal Stomach	stomach
27	chr12:48415600-48415800	Active TSS	Rectal Mucosa Donor 29	rectum
28	chr12:48415600-48415800	Flanking Active TSS	A549	lung
29	chr12:48415600-48416000	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr12:48415600-48416600	Weak transcription	Left Ventricle	heart

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