Variant report

Variant	rs725454
Chromosome Location	chr12:48502100-48502101
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:48500571..48503072-chr12:48556879..48559027,2	K562	blood:
2	chr12:48501965..48505279-chr12:48511816..48514639,4	K562	blood:
3	chr12:48500761..48502432-chr12:48514527..48516446,2	MCF-7	breast:
4	chr12:48497586..48502171-chr12:48511099..48514258,8	MCF-7	breast:
5	chr12:48499494..48502600-chr12:48549917..48552067,4	MCF-7	breast:
6	chr12:48495831..48503326-chr12:48548997..48555180,8	K562	blood:

Variant related genes	Relation type
ENSG00000152556	Chromatin interaction
ENSG00000258051	Chromatin interaction
ENSG00000177981	Chromatin interaction

Extended variants
information (count: 122 )
Associated
traits (count: 14 )

rSNPs within LD-proxies of this variant (count:119)

rs_ID	r²[population]
rs10082861	0.88[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs10219623	0.94[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.85[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs10219645	0.83[ASN][1000 genomes]
rs10467101	0.81[CHB][hapmap];0.84[JPT][hapmap]
rs10875724	0.93[JPT][hapmap]
rs10875725	0.85[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap]
rs10875730	0.81[EUR][1000 genomes]
rs10875731	0.83[EUR][1000 genomes]
rs10875732	0.92[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs10875735	0.92[CEU][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10875736	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10875737	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10875738	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10875740	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10875745	0.80[ASW][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.89[MKK][hapmap];0.93[YRI][hapmap];0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs10875746	0.89[CHB][hapmap];0.88[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.85[TSI][hapmap];0.81[YRI][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10875747	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10875748	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10875750	1.00[CEU][hapmap];0.94[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10875756	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10875762	0.81[EUR][1000 genomes]
rs10875767	0.81[CHB][hapmap];0.93[JPT][hapmap]
rs10875770	0.83[CHB][hapmap];0.82[CHD][hapmap];0.93[JPT][hapmap]
rs10875772	0.83[CHB][hapmap];0.82[CHD][hapmap];0.93[JPT][hapmap];0.82[MEX][hapmap]
rs10875792	0.85[JPT][hapmap]
rs10875793	0.92[JPT][hapmap]
rs11168355	0.83[CHD][hapmap];1.00[GIH][hapmap];0.85[TSI][hapmap]
rs11168357	0.82[CHD][hapmap];0.96[GIH][hapmap];0.93[JPT][hapmap];0.85[TSI][hapmap]
rs11168369	0.86[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs11168370	0.82[EUR][1000 genomes]
rs11168371	0.93[CEU][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.88[MKK][hapmap];0.90[TSI][hapmap];0.81[EUR][1000 genomes]
rs11168374	0.83[EUR][1000 genomes]
rs11168383	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11168386	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11168401	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11168403	0.85[CEU][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11168413	0.94[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs11168414	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11168415	0.91[ASN][1000 genomes]
rs11168416	0.91[ASN][1000 genomes]
rs11168418	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11168420	0.89[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11168421	0.89[CHB][hapmap];0.84[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs11168422	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11168425	0.89[CHB][hapmap];0.94[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs11168427	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11168433	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.97[TSI][hapmap];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11168450	0.89[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap]
rs11168459	0.83[CHB][hapmap];0.82[CHD][hapmap];0.93[JPT][hapmap]
rs11168516	0.87[JPT][hapmap]
rs11558768	0.82[EUR][1000 genomes]
rs12296244	0.83[EUR][1000 genomes]
rs12297004	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12297470	0.80[ASW][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.86[YRI][hapmap];0.85[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs12301339	0.89[CEU][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12304476	0.93[CEU][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12305182	0.93[JPT][hapmap]
rs12305511	0.93[CEU][hapmap];0.94[CHB][hapmap];0.88[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.85[MKK][hapmap];0.94[TSI][hapmap];0.83[EUR][1000 genomes]
rs12305647	0.83[EUR][1000 genomes]
rs12306290	0.88[ASN][1000 genomes]
rs12306451	0.93[CEU][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.89[MKK][hapmap];0.97[TSI][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12310813	0.80[ASW][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.86[YRI][hapmap];0.85[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs12310999	0.83[EUR][1000 genomes]
rs12311774	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12311953	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12312134	0.94[CHB][hapmap];0.93[JPT][hapmap];0.85[YRI][hapmap];0.87[ASN][1000 genomes]
rs12313300	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12313404	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12315625	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17122620	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17122666	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17122812	0.83[CHB][hapmap];0.93[JPT][hapmap]
rs1859445	0.80[ASW][hapmap];0.94[CHB][hapmap];0.91[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.86[YRI][hapmap];0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2012773	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs2079295	0.85[CHB][hapmap];0.93[JPT][hapmap]
rs2107638	0.89[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2158516	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2228500	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2269933	0.89[CHB][hapmap];0.89[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs2269935	1.00[CEU][hapmap];0.94[CHB][hapmap];0.88[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2269936	0.85[CEU][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs2279464	0.87[JPT][hapmap]
rs2286021	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3782910	0.93[CEU][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3782911	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4760609	0.83[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.84[MEX][hapmap];0.85[TSI][hapmap]
rs4760619	0.81[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs4760622	0.93[CEU][hapmap];0.94[CHB][hapmap];0.88[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.83[MKK][hapmap];0.94[TSI][hapmap];0.85[YRI][hapmap];0.83[EUR][1000 genomes]
rs4760680	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4760681	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4760684	0.91[ASN][1000 genomes]
rs4760687	0.89[CHB][hapmap];0.94[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs4760689	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4760690	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4760695	0.93[CEU][hapmap];0.94[CHB][hapmap];0.88[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.81[MKK][hapmap];0.94[TSI][hapmap];0.82[EUR][1000 genomes]
rs4760696	0.89[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap]
rs4760697	0.89[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap]
rs58952582	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs60106007	0.91[ASN][1000 genomes]
rs60761335	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs61343568	0.85[ASN][1000 genomes]
rs61918774	0.83[EUR][1000 genomes]
rs61918806	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs61918809	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs61918810	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6580659	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs7135779	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs719008	0.93[JPT][hapmap]
rs7299135	0.83[CHD][hapmap];0.93[JPT][hapmap]
rs7299271	0.83[CHD][hapmap];0.93[JPT][hapmap]
rs73102065	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs73102067	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7485355	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7486424	0.89[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs7964359	0.81[CHB][hapmap]
rs8804	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs886588	0.93[CEU][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9634261	0.87[JPT][hapmap]
rs989144	0.93[CEU][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]

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	esv2758307	chr12:48429702-48825499	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
2	esv2759898	chr12:48429702-48825499	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
3	nsv508673	chr12:48489786-48567138	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:14)

SNP	Gene	Cis/trans	Tissue	Source
rs725454	RP1-228P16.1	cis	Skin Sun Exposed Lower leg	GTEx
rs725454	LMBR1L	cis	cerebellum	SCAN
rs725454	FAM186B	cis	parietal	SCAN
rs725454	RP1-228P16.1	cis	Adipose Subcutaneous	GTEx
rs725454	RP1-228P16.1	cis	Artery Tibial	GTEx
rs725454	LOC255411	cis	cerebellum	SCAN
rs725454	RP1-228P16.1	cis	Thyroid	GTEx
rs725454	PRKAG1	cis	parietal	SCAN
rs725454	SENP1	cis	cerebellum	SCAN
rs725454	H1FNT	cis	cerebellum	SCAN
rs725454	RP1-228P16.1	cis	Heart Left Ventricle	GTEx
rs725454	ASB8	cis	cerebellum	SCAN
rs725454	ASB8	cis	parietal	SCAN
rs725454	SENP1	cis	parietal	SCAN

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:48500800-48502200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
2	chr12:48500800-48502200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
3	chr12:48501000-48503600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr12:48501000-48504000	Weak transcription	Psoas Muscle	Psoas
5	chr12:48501000-48504200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr12:48501000-48504800	Weak transcription	Lung	lung
7	chr12:48501000-48508800	Weak transcription	K562	blood
8	chr12:48501200-48503000	Weak transcription	HMEC	breast
9	chr12:48501200-48503200	Weak transcription	Hela-S3	cervix
10	chr12:48501200-48503400	Weak transcription	Skeletal Muscle Female	skeletal muscle
11	chr12:48501200-48503400	Weak transcription	Spleen	Spleen
12	chr12:48501200-48504600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr12:48501200-48512200	Weak transcription	Duodenum Mucosa	Duodenum
14	chr12:48501400-48503800	Weak transcription	Skeletal Muscle Male	skeletal muscle
15	chr12:48501600-48506600	Weak transcription	Fetal Intestine Small	intestine
16	chr12:48501800-48503200	Weak transcription	HepG2	liver
17	chr12:48502000-48503400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
18	chr12:48502000-48503800	Enhancers	GM12878-XiMat	blood

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