Variant report

Variant	rs6580650
Chromosome Location	chr12:48418556-48418557
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:5)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:48415272..48418773-chr12:48419086..48422802,6	MCF-7	breast:
2	chr12:48418539..48420191-chr12:48595608..48598283,2	K562	blood:
3	chr12:48417372..48419126-chr12:48439664..48441801,2	MCF-7	breast:
4	chr12:48416195..48418689-chr12:48432533..48434686,2	K562	blood:
5	chr12:48416900..48419304-chr12:48549157..48552214,3	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
ENSG00000177981	Chromatin interaction
ENSG00000172640	Chromatin interaction
ENSG00000257955	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10875716	0.88[CEU][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10875718	0.88[CEU][hapmap];0.93[GIH][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap];0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10875719	0.88[CEU][hapmap];0.97[GIH][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap];0.92[EUR][1000 genomes]
rs10875721	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10875743	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs10875749	0.92[CEU][hapmap]
rs10875753	0.92[CEU][hapmap];0.95[GIH][hapmap];0.83[MEX][hapmap];0.87[TSI][hapmap]
rs11168291	1.00[CHD][hapmap]
rs11168343	0.81[EUR][1000 genomes]
rs11168351	0.88[CEU][hapmap];0.91[TSI][hapmap];0.93[EUR][1000 genomes]
rs11168408	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs11168428	0.89[ASW][hapmap];0.92[CEU][hapmap];0.98[GIH][hapmap];0.83[MEX][hapmap];0.87[TSI][hapmap]
rs11168437	0.88[CEU][hapmap];0.95[GIH][hapmap];0.83[MEX][hapmap];0.87[TSI][hapmap]
rs12228750	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs12368659	0.92[CEU][hapmap]
rs12816820	0.92[CEU][hapmap]
rs1476607	0.92[CEU][hapmap];0.98[GIH][hapmap];0.92[MEX][hapmap];0.87[TSI][hapmap]
rs1635554	1.00[CHD][hapmap]
rs2051851	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs2408955	0.86[GIH][hapmap]
rs3997	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs4760612	1.00[CEU][hapmap];0.87[YRI][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4760679	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs6580652	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7139330	0.80[EUR][1000 genomes]
rs7301003	1.00[ASW][hapmap];0.92[CEU][hapmap];0.98[GIH][hapmap];0.83[MEX][hapmap];0.87[TSI][hapmap]
rs7315820	0.83[GIH][hapmap]
rs7486941	0.81[CEU][hapmap];0.90[GIH][hapmap]
rs7487682	0.88[ASW][hapmap];0.81[CEU][hapmap];0.90[GIH][hapmap]
rs7971880	0.88[CEU][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.84[EUR][1000 genomes]
rs7975632	1.00[CEU][hapmap];0.95[GIH][hapmap];0.92[MEX][hapmap];0.84[TSI][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs8716	1.00[ASW][hapmap];0.92[CEU][hapmap];0.98[GIH][hapmap];1.00[LWK][hapmap];0.83[MEX][hapmap];0.84[MKK][hapmap];0.87[TSI][hapmap];0.87[YRI][hapmap]
rs973398	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs9971924	0.81[EUR][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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs6580650	OR6C70	trans	parietal	SCAN
rs6580650	H1FNT	cis	Muscle Skeletal	GTEx
rs6580650	RP1-228P16.1	cis	Artery Tibial	GTEx
rs6580650	PRPF40B	cis	parietal	SCAN
rs6580650	DDX23	cis	parietal	SCAN
rs6580650	RPAP3	cis	cerebellum	SCAN

Chromatin state (count:18 , 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	chr12:48418000-48419000	Weak transcription	HepG2	liver
10	chr12:48418000-48420200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr12:48418000-48422200	Weak transcription	Fetal Heart	heart
12	chr12:48418200-48418600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr12:48418200-48418600	Weak transcription	Fetal Intestine Large	intestine
14	chr12:48418200-48418600	Weak transcription	Fetal Intestine Small	intestine
15	chr12:48418200-48422200	Weak transcription	Skeletal Muscle Female	skeletal muscle
16	chr12:48418200-48424200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr12:48418400-48419600	Bivalent Enhancer	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr12:48418400-48425800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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