Variant report

Variant	rs10875725
Chromosome Location	chr12:48424497-48424498
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:48422786..48426072-chr12:48430482..48433177,3	MCF-7	breast:
2	chr12:48416331..48419438-chr12:48423378..48425988,3	K562	blood:
3	chr12:48421744..48425259-chr12:48425932..48429243,5	MCF-7	breast:
4	chr12:48422677..48425414-chr12:48434042..48436175,2	MCF-7	breast:
5	chr12:48424222..48426815-chr12:48427012..48429829,3	K562	blood:

Variant related genes	Relation type
ENSG00000257955	Chromatin interaction

Extended variants
information (count: 88 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:87)

rs_ID	r²[population]
rs10082861	0.82[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap]
rs10219623	1.00[JPT][hapmap]
rs10467101	0.84[JPT][hapmap]
rs10875720	0.91[ASN][1000 genomes]
rs10875722	0.91[ASN][1000 genomes]
rs10875723	0.92[ASN][1000 genomes]
rs10875724	0.94[CHB][hapmap];0.93[JPT][hapmap];0.95[ASN][1000 genomes]
rs10875730	0.98[ASN][1000 genomes]
rs10875731	0.98[ASN][1000 genomes]
rs10875732	0.94[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs10875735	0.82[ASN][1000 genomes]
rs10875745	0.96[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.91[TSI][hapmap]
rs10875746	0.85[GIH][hapmap];1.00[JPT][hapmap]
rs10875750	0.93[GIH][hapmap];1.00[JPT][hapmap]
rs10875767	0.93[JPT][hapmap]
rs10875770	0.93[JPT][hapmap]
rs10875772	0.93[JPT][hapmap]
rs11168355	0.90[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];0.90[ASN][1000 genomes]
rs11168357	0.90[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];0.93[JPT][hapmap];0.92[ASN][1000 genomes]
rs11168369	0.94[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs11168371	0.95[CHB][hapmap];0.94[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.98[ASN][1000 genomes]
rs11168374	0.98[ASN][1000 genomes]
rs11168383	0.82[ASN][1000 genomes]
rs11168386	0.82[ASN][1000 genomes]
rs11168403	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs11168413	1.00[JPT][hapmap]
rs11168414	0.93[GIH][hapmap];1.00[JPT][hapmap]
rs11168418	0.93[GIH][hapmap];1.00[JPT][hapmap]
rs11168420	0.93[GIH][hapmap];1.00[JPT][hapmap]
rs11168421	0.86[ASW][hapmap];0.83[CEU][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.82[YRI][hapmap]
rs11168425	0.86[ASW][hapmap];0.83[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.82[YRI][hapmap]
rs11168427	0.93[GIH][hapmap];1.00[JPT][hapmap]
rs11168433	0.93[GIH][hapmap];1.00[JPT][hapmap]
rs11168450	1.00[JPT][hapmap]
rs11168459	0.93[JPT][hapmap]
rs12296244	0.98[ASN][1000 genomes]
rs12297004	0.82[ASN][1000 genomes]
rs12297470	1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.91[TSI][hapmap]
rs12304476	0.95[CHB][hapmap];0.91[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap]
rs12305182	0.93[JPT][hapmap];0.96[ASN][1000 genomes]
rs12305511	0.81[GIH][hapmap];1.00[JPT][hapmap]
rs12306451	0.95[CHB][hapmap];0.94[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap]
rs12310813	1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.91[TSI][hapmap]
rs12310999	0.98[ASN][1000 genomes]
rs12311774	0.82[ASN][1000 genomes]
rs12311953	0.82[ASN][1000 genomes]
rs12312134	0.93[JPT][hapmap]
rs12313300	0.82[ASN][1000 genomes]
rs17122620	0.82[ASN][1000 genomes]
rs17122666	0.85[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap]
rs17122812	0.93[JPT][hapmap]
rs1859445	1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.89[TSI][hapmap]
rs2012773	1.00[JPT][hapmap]
rs2079295	0.86[CHB][hapmap];0.93[JPT][hapmap];0.90[ASN][1000 genomes]
rs2107638	1.00[JPT][hapmap]
rs2228500	0.82[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap]
rs2269933	0.86[ASW][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap];0.82[YRI][hapmap]
rs2269935	1.00[JPT][hapmap]
rs2269936	0.95[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs28459711	0.91[ASN][1000 genomes]
rs3782910	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs4760609	0.90[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];0.93[JPT][hapmap];0.93[ASN][1000 genomes]
rs4760610	0.94[ASN][1000 genomes]
rs4760619	1.00[JPT][hapmap]
rs4760622	0.81[GIH][hapmap];1.00[JPT][hapmap]
rs4760676	0.96[ASN][1000 genomes]
rs4760680	0.82[ASN][1000 genomes]
rs4760681	0.89[GIH][hapmap];1.00[JPT][hapmap]
rs4760687	0.86[ASW][hapmap];0.83[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.82[YRI][hapmap]
rs4760695	0.81[GIH][hapmap];1.00[JPT][hapmap]
rs4760696	1.00[JPT][hapmap]
rs4760697	1.00[JPT][hapmap]
rs58952582	0.82[ASN][1000 genomes]
rs60761335	0.82[ASN][1000 genomes]
rs61918774	0.98[ASN][1000 genomes]
rs6580659	1.00[JPT][hapmap]
rs7135779	1.00[JPT][hapmap]
rs719008	0.90[CHB][hapmap];0.93[JPT][hapmap];0.91[ASN][1000 genomes]
rs725454	0.85[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap]
rs7299135	0.90[CHB][hapmap];0.97[CHD][hapmap];0.93[JPT][hapmap];0.91[ASN][1000 genomes]
rs7299271	0.90[CHB][hapmap];0.97[CHD][hapmap];0.93[JPT][hapmap];0.91[ASN][1000 genomes]
rs7299364	0.91[ASN][1000 genomes]
rs7486424	0.83[CEU][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap]
rs7964359	0.87[CHB][hapmap];0.83[ASN][1000 genomes]
rs8804	0.93[GIH][hapmap];1.00[JPT][hapmap]
rs886588	0.94[CHB][hapmap];0.94[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap]
rs989144	0.95[CHB][hapmap];1.00[JPT][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:7)

SNP	Gene	Cis/trans	Tissue	Source
rs10875725	RPAP3	cis	cerebellum	SCAN
rs10875725	SENP1	cis	parietal	SCAN
rs10875725	RP1-228P16.1	cis	Thyroid	GTEx
rs10875725	AQP6	cis	parietal	SCAN
rs10875725	C12orf41	cis	parietal	SCAN
rs10875725	RP1-228P16.1	cis	Artery Tibial	GTEx
rs10875725	RP1-228P16.1	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:48418400-48425800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr12:48418600-48425200	Enhancers	Fetal Intestine Large	intestine
3	chr12:48420400-48429000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr12:48420800-48424600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr12:48421400-48425000	Enhancers	Fetal Intestine Small	intestine
6	chr12:48421600-48425000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr12:48422000-48429000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr12:48422200-48424800	Enhancers	Skeletal Muscle Female	skeletal muscle
9	chr12:48422200-48425000	Enhancers	Fetal Heart	heart
10	chr12:48422400-48424800	Enhancers	K562	blood
11	chr12:48422600-48426600	Enhancers	Breast Myoepithelial Primary Cells	Breast
12	chr12:48422800-48438800	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr12:48423800-48425400	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell
14	chr12:48423800-48430600	Weak transcription	Fetal Kidney	kidney
15	chr12:48423800-48430600	Weak transcription	Right Atrium	heart
16	chr12:48424000-48424600	Genic enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr12:48424000-48425600	Enhancers	HMEC	breast
18	chr12:48424000-48429000	Weak transcription	Fetal Lung	lung
19	chr12:48424200-48430000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr12:48424200-48430200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr12:48424400-48425400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr12:48424400-48427400	Weak transcription	Right Ventricle	heart
23	chr12:48424400-48430600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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