Variant report

Variant	rs10875716
Chromosome Location	chr12:48389023-48389024
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:48346353..48348105-chr12:48388384..48390746,2	MCF-7	breast:
2	chr12:48387141..48389064-chr12:48389409..48391360,2	MCF-7	breast:
3	chr12:48375884..48381022-chr12:48386743..48391938,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000139219	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 9 )

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

rs_ID	r²[population]
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	0.82[AMR][1000 genomes];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	0.83[LWK][hapmap];0.91[TSI][hapmap];0.82[EUR][1000 genomes]
rs11168343	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11168351	1.00[ASW][hapmap];0.92[CEU][hapmap];0.98[TSI][hapmap];0.89[EUR][1000 genomes]
rs11168408	0.88[CEU][hapmap]
rs11168411	1.00[LWK][hapmap];0.81[MKK][hapmap]
rs11168428	0.81[CEU][hapmap];0.84[MEX][hapmap]
rs11168437	0.82[ASW][hapmap];1.00[LWK][hapmap];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	0.95[EUR][1000 genomes]
rs1476607	0.82[ASW][hapmap];0.81[CEU][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap]
rs1793957	1.00[CHB][hapmap];0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2051851	0.88[CEU][hapmap]
rs3997	0.88[CEU][hapmap]
rs4760612	0.87[CEU][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4760679	0.88[CEU][hapmap]
rs6580650	0.88[CEU][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7301003	0.81[CEU][hapmap];0.84[MEX][hapmap]
rs7971880	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]
rs7975632	0.82[ASW][hapmap];0.88[CEU][hapmap];1.00[LWK][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:3 , 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	nsv899061	chr12:48360620-48389023	Bivalent Enhancer Enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
3	nsv519659	chr12:48366449-48389245	Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs10875716	RP1-228P16.1	cis	Artery Tibial	GTEx
rs10875716	CCNT1	cis	cerebellum	SCAN
rs10875716	PRPF40B	cis	parietal	SCAN
rs10875716	C12orf68	cis	parietal	SCAN
rs10875716	OR6C70	trans	parietal	SCAN
rs10875716	H1FNT	cis	Muscle Skeletal	GTEx
rs10875716	LMBR1L	cis	cerebellum	SCAN
rs10875716	DDX23	cis	parietal	SCAN
rs10875716	TAF2	cis	Frontal Cortex	GTEx

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:48376800-48391000	Weak transcription	Fetal Intestine Large	intestine
2	chr12:48382800-48394600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr12:48383800-48393800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr12:48383800-48394400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr12:48385200-48391600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr12:48385600-48389600	Weak transcription	Right Atrium	heart
7	chr12:48385800-48389600	Weak transcription	Left Ventricle	heart
8	chr12:48385800-48389600	Weak transcription	Lung	lung
9	chr12:48386000-48389600	Weak transcription	Right Ventricle	heart
10	chr12:48386400-48389800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
11	chr12:48386800-48392800	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr12:48387000-48391600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr12:48387600-48390200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr12:48388000-48391400	Enhancers	Fetal Brain Male	brain
15	chr12:48388600-48389400	Bivalent Enhancer	Fetal Lung	lung
16	chr12:48388600-48389400	Weak transcription	Psoas Muscle	Psoas
17	chr12:48388600-48390400	Enhancers	Brain Germinal Matrix	brain
18	chr12:48388800-48389400	Bivalent Enhancer	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr12:48388800-48390200	Strong transcription	Fetal Intestine Small	intestine
20	chr12:48389000-48390600	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr12:48389000-48390600	Enhancers	Skeletal Muscle Female	skeletal muscle

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