Variant report

Variant	rs7971880
Chromosome Location	chr12:48391055-48391056
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:48384703..48387276-chr12:48389834..48391406,2	K562	blood:
2	chr12:48390214..48392047-chr12:48396336..48398947,2	K562	blood:
3	chr12:48387141..48389064-chr12:48389409..48391360,2	MCF-7	breast:
4	chr12:48389851..48391861-chr12:48407332..48409151,2	MCF-7	breast:
5	chr12:48389997..48392047-chr12:48397447..48399843,2	K562	blood:
6	chr12:48375884..48381022-chr12:48386743..48391938,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000139219	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 9 )

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

rs_ID	r²[population]
rs10875716	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10875718	0.84[CEU][hapmap];0.92[MEX][hapmap];0.93[TSI][hapmap];0.84[EUR][1000 genomes]
rs10875719	0.84[CEU][hapmap];0.92[MEX][hapmap];0.93[TSI][hapmap];0.84[EUR][1000 genomes]
rs10875721	0.85[EUR][1000 genomes]
rs10875743	0.88[CEU][hapmap]
rs10875749	0.81[CEU][hapmap]
rs10875753	0.81[CEU][hapmap];0.84[MEX][hapmap]
rs11168338	0.91[TSI][hapmap];0.81[EUR][1000 genomes]
rs11168343	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11168351	0.84[ASW][hapmap];0.92[CEU][hapmap];0.98[TSI][hapmap];0.89[EUR][1000 genomes]
rs11168408	0.88[CEU][hapmap]
rs11168411	0.81[MKK][hapmap]
rs11168428	0.81[CEU][hapmap];0.84[MEX][hapmap]
rs11168437	0.84[MEX][hapmap]
rs12228750	0.88[CEU][hapmap]
rs12368659	0.81[CEU][hapmap]
rs12811832	0.86[TSI][hapmap]
rs12816820	0.81[CEU][hapmap]
rs12817104	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1476607	0.81[CEU][hapmap];0.92[MEX][hapmap]
rs1793957	1.00[CHB][hapmap];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2051851	0.88[CEU][hapmap]
rs3997	0.88[CEU][hapmap]
rs4760612	0.87[CEU][hapmap];0.83[EUR][1000 genomes]
rs4760679	0.88[CEU][hapmap]
rs6580650	0.88[CEU][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.84[EUR][1000 genomes]
rs7301003	0.81[CEU][hapmap];0.84[MEX][hapmap]
rs7975632	0.88[CEU][hapmap];0.92[MEX][hapmap];0.81[EUR][1000 genomes]
rs8716	0.81[CEU][hapmap];0.84[MEX][hapmap]
rs973398	0.88[CEU][hapmap]

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:9)

SNP	Gene	Cis/trans	Tissue	Source
rs7971880	RP1-228P16.1	cis	Artery Tibial	GTEx
rs7971880	PRPF40B	cis	parietal	SCAN
rs7971880	DDX23	cis	parietal	SCAN
rs7971880	TAF2	cis	Frontal Cortex	GTEx
rs7971880	LMBR1L	cis	cerebellum	SCAN
rs7971880	H1FNT	cis	Muscle Skeletal	GTEx
rs7971880	C12orf68	cis	parietal	SCAN
rs7971880	CCNT1	cis	cerebellum	SCAN
rs7971880	OR6C70	trans	parietal	SCAN

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:48382800-48394600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
2	chr12:48383800-48393800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr12:48383800-48394400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr12:48385200-48391600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr12:48386800-48392800	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr12:48387000-48391600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr12:48388000-48391400	Enhancers	Fetal Brain Male	brain
8	chr12:48389800-48391200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
9	chr12:48389800-48391800	Enhancers	Liver	Liver
10	chr12:48390000-48395000	Weak transcription	Right Atrium	heart
11	chr12:48390200-48391200	Weak transcription	Placenta	Placenta
12	chr12:48390200-48391800	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr12:48390400-48394600	Weak transcription	Left Ventricle	heart
14	chr12:48390400-48394600	Weak transcription	Right Ventricle	heart
15	chr12:48390600-48391800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr12:48391000-48391200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr12:48391000-48391400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr12:48391000-48391600	Enhancers	HMEC	breast
19	chr12:48391000-48391800	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain

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