Variant report

Variant	rs11172367
Chromosome Location	chr12:58272486-58272487
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:58272183..58275031-chr12:58279925..58281900,3	K562	blood:
2	chr12:58271722..58273746-chr12:58285957..58287603,2	MCF-7	breast:
3	chr12:58163873..58166581-chr12:58271656..58273693,2	K562	blood:

Variant related genes	Relation type
ENSG00000123427	Chromatin interaction
ENSG00000037897	Chromatin interaction

Extended variants
information (count: 78 )
Associated
traits (count: 16 )

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs10431552	0.83[JPT][hapmap]
rs10444569	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10747783	0.83[JPT][hapmap]
rs10747784	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10747786	1.00[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.97[TSI][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10747787	1.00[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.97[TSI][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10783847	0.83[JPT][hapmap]
rs10783848	0.80[JPT][hapmap]
rs10783850	0.87[JPT][hapmap];0.82[AMR][1000 genomes]
rs10783851	0.81[CHD][hapmap];0.87[JPT][hapmap];0.82[AMR][1000 genomes]
rs10783854	0.87[JPT][hapmap];0.85[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs10783855	0.84[CHD][hapmap];0.87[JPT][hapmap];0.87[MEX][hapmap];0.81[TSI][hapmap];0.87[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs10783856	0.85[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs10877012	0.83[JPT][hapmap]
rs10877014	0.83[JPT][hapmap]
rs10877015	0.83[JPT][hapmap]
rs10877016	0.83[JPT][hapmap]
rs10877019	0.83[JPT][hapmap]
rs10877024	0.82[AMR][1000 genomes]
rs10877025	0.82[AMR][1000 genomes]
rs10877026	0.81[AMR][1000 genomes]
rs10877028	0.84[CHD][hapmap];0.87[GIH][hapmap];0.87[JPT][hapmap];0.92[MEX][hapmap];0.81[TSI][hapmap]
rs10877029	0.88[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.90[TSI][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10877030	0.88[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.90[TSI][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10877031	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10877032	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11172333	0.83[JPT][hapmap]
rs11172335	0.83[JPT][hapmap]
rs11172343	0.83[JPT][hapmap]
rs11172344	0.83[JPT][hapmap]
rs11172349	0.83[JPT][hapmap]
rs11172351	0.83[JPT][hapmap]
rs11172368	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11172369	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11172371	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11172375	0.82[ASN][1000 genomes]
rs11172378	0.87[CHD][hapmap];0.83[MEX][hapmap];0.82[ASN][1000 genomes]
rs12312955	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12319233	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12426201	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1599750	0.83[CHD][hapmap];0.86[GIH][hapmap];0.88[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs1599751	0.80[CHD][hapmap];0.87[GIH][hapmap];0.87[JPT][hapmap];0.96[MEX][hapmap];0.81[TSI][hapmap];0.88[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs1599931	0.93[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1875124	0.83[JPT][hapmap]
rs1875125	0.94[JPT][hapmap];0.81[AMR][1000 genomes]
rs1962047	0.90[CHD][hapmap];0.83[MEX][hapmap];0.83[ASN][1000 genomes]
rs2002275	0.96[CEU][hapmap];0.90[CHD][hapmap];0.92[MEX][hapmap];0.97[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3751331	0.83[ASN][1000 genomes]
rs3825079	0.83[JPT][hapmap]
rs4237844	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.97[TSI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4237845	0.90[CHD][hapmap]
rs4630335	0.81[CHD][hapmap]
rs4646536	0.83[JPT][hapmap]
rs4760171	0.84[GIH][hapmap];0.87[JPT][hapmap]
rs4760172	0.88[CEU][hapmap];0.94[CHB][hapmap];0.93[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.90[TSI][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4760332	0.94[JPT][hapmap]
rs4760335	0.80[AMR][1000 genomes]
rs4760339	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4760340	0.81[CHB][hapmap];1.00[CHD][hapmap];0.80[ASN][1000 genomes]
rs4760341	0.94[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs5017863	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs59401446	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6581155	0.83[JPT][hapmap]
rs6581157	0.84[ASN][1000 genomes]
rs703842	0.83[JPT][hapmap]
rs7134797	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs724834	0.83[JPT][hapmap]
rs7312623	1.00[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.97[TSI][hapmap];0.85[YRI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7489290	0.92[JPT][hapmap];0.80[AMR][1000 genomes]
rs7954957	0.90[CHD][hapmap]
rs7969844	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7971877	0.80[CHD][hapmap]
rs8181644	0.83[JPT][hapmap]
rs870392	0.80[CHD][hapmap];0.94[JPT][hapmap]
rs871871	0.80[CHD][hapmap];0.84[GIH][hapmap];0.94[JPT][hapmap]
rs923829	0.83[JPT][hapmap]
rs9645819	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][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	nsv559046	chr12:58162085-58478598	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	261 gene(s)	inside rSNPs	diseases

mRNA abundance (count:16)

SNP	Gene	Cis/trans	Tissue	Source
rs11172367	XRCC6BP1	cis	Whole Blood	GTEx
rs11172367	XRCC6BP1	cis	Heart Left Ventricle	GTEx
rs11172367	TSFM	Cis_1M	lymphoblastoid	RTeQTL
rs11172367	XRCC6BP1	cis	Skin Sun Exposed Lower leg	GTEx
rs11172367	METTL21B	cis	lung	GTEx
rs11172367	XRCC6BP1	cis	Muscle Skeletal	GTEx
rs11172367	FAM119B	cis	lymphoblastoid	seeQTL
rs11172367	TSFM	cis	parietal	SCAN
rs11172367	TSFM	cis	lymphoblastoid	seeQTL
rs11172367	XRCC6BP1	cis	Artery Tibial	GTEx
rs11172367	FAM119B	cis	cerebellum	SCAN
rs11172367	CDK2	cis	parietal	SCAN
rs11172367	XRCC6BP1	cis	lung	GTEx
rs11172367	XRCC6BP1	cis	lymphoblastoid	seeQTL
rs11172367	XRCC6BP1	Cis_1M	lymphoblastoid	RTeQTL
rs11172367	XRCC6BP1	cis	Adipose Subcutaneous	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:58263600-58275000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr12:58268400-58275000	Weak transcription	Fetal Muscle Leg	muscle
3	chr12:58268800-58275200	Weak transcription	Duodenum Mucosa	Duodenum
4	chr12:58268800-58275600	Weak transcription	Stomach Mucosa	stomach
5	chr12:58270000-58275200	Weak transcription	NHDF-Ad	bronchial
6	chr12:58270000-58275400	Weak transcription	K562	blood
7	chr12:58270000-58276200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr12:58270200-58274200	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr12:58270200-58275000	Weak transcription	NHLF	lung
10	chr12:58270200-58276600	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr12:58270400-58274400	Weak transcription	Skeletal Muscle Male	skeletal muscle
12	chr12:58270400-58274600	Weak transcription	Osteobl	bone
13	chr12:58270400-58275000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr12:58270400-58275200	Weak transcription	Left Ventricle	heart
15	chr12:58270400-58276600	Weak transcription	Psoas Muscle	Psoas
16	chr12:58270400-58280600	Weak transcription	Colonic Mucosa	Colon
17	chr12:58270600-58275000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr12:58270600-58275000	Weak transcription	Skeletal Muscle Female	skeletal muscle
19	chr12:58270600-58275200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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