Variant report

Variant	rs4760610
Chromosome Location	chr12:48418225-48418226
allele	C/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:8)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:48415272..48418773-chr12:48419086..48422802,6	MCF-7	breast:
2	chr12:48415815..48418237-chr12:48421031..48422834,2	K562	blood:
3	chr12:48406038..48410831-chr12:48411860..48418424,9	MCF-7	breast:
4	chr12:48391315..48400584-chr12:48411914..48418489,16	MCF-7	breast:
5	chr12:48417372..48419126-chr12:48439664..48441801,2	MCF-7	breast:
6	chr12:48416195..48418689-chr12:48432533..48434686,2	K562	blood:
7	chr12:48416900..48419304-chr12:48549157..48552214,3	MCF-7	breast:
8	chr12:48416842..48418454-chr12:48435864..48437741,2	MCF-7	breast:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TMEM106C-1	chr12:48416618-48419252	ENSG00000257985.1

No data

Variant related genes	Relation type
ENSG00000257955	Chromatin interaction
ENSG00000177981	Chromatin interaction
ENSG00000139219	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs10875720	0.96[ASN][1000 genomes]
rs10875722	0.96[ASN][1000 genomes]
rs10875723	0.97[ASN][1000 genomes]
rs10875724	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10875725	0.94[ASN][1000 genomes]
rs10875728	0.80[EUR][1000 genomes]
rs10875729	0.80[EUR][1000 genomes]
rs10875730	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10875731	0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs10875732	0.86[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs11168355	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11168357	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11168369	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11168371	0.94[ASN][1000 genomes]
rs11168374	0.86[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs12296244	0.86[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs12305182	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12310999	0.86[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs1990028	0.87[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs2079295	0.95[ASN][1000 genomes]
rs2269936	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28459711	0.96[ASN][1000 genomes]
rs4760609	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4760676	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61918774	0.86[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs719008	0.96[ASN][1000 genomes]
rs7299135	0.96[ASN][1000 genomes]
rs7299271	0.96[ASN][1000 genomes]
rs7299364	0.96[ASN][1000 genomes]
rs7964359	0.87[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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4760610	RP1-228P16.1	cis	Thyroid	GTEx
rs4760610	RP1-228P16.1	cis	Adipose Subcutaneous	GTEx
rs4760610	RP1-228P16.1	cis	Skin Sun Exposed Lower leg	GTEx
rs4760610	RP1-228P16.1	cis	Artery Tibial	GTEx

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:48415800-48420400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr12:48416800-48423400	Weak transcription	Right Atrium	heart
3	chr12:48417000-48418600	Weak transcription	Right Ventricle	heart
4	chr12:48417400-48419000	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
5	chr12:48417600-48420800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr12:48417800-48419200	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr12:48417800-48421400	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr12:48417800-48423400	Weak transcription	Fetal Lung	lung
9	chr12:48418000-48418400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr12:48418000-48419000	Weak transcription	HepG2	liver
11	chr12:48418000-48420200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr12:48418000-48422200	Weak transcription	Fetal Heart	heart
13	chr12:48418200-48418600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr12:48418200-48418600	Weak transcription	Fetal Intestine Large	intestine
15	chr12:48418200-48418600	Weak transcription	Fetal Intestine Small	intestine
16	chr12:48418200-48422200	Weak transcription	Skeletal Muscle Female	skeletal muscle
17	chr12:48418200-48424200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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