Variant report

Variant	rs11172369
Chromosome Location	chr12:58280592-58280593
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:58273580..58278130-chr12:58279194..58284140,7	MCF-7	breast:
2	chr12:58238917..58240911-chr12:58280507..58282543,2	K562	blood:
3	chr12:58272183..58275031-chr12:58279925..58281900,3	K562	blood:
4	chr12:58273430..58275721-chr12:58280183..58281805,2	MCF-7	breast:
5	chr12:58279797..58285277-chr12:58286449..58291551,8	K562	blood:
6	chr12:58233944..58243826-chr12:58273095..58290464,46	MCF-7	breast:
7	chr12:58269021..58271713-chr12:58278735..58281292,2	MCF-7	breast:
8	chr12:58275772..58278261-chr12:58278703..58280624,2	MCF-7	breast:
9	chr12:58227798..58230136-chr12:58279373..58282138,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000245651	Chromatin interaction
ENSG00000175215	Chromatin interaction

Extended variants
information (count: 76 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:75)

rs_ID	r²[population]
rs10431552	0.83[JPT][hapmap]
rs10444569	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10747783	0.84[JPT][hapmap]
rs10747784	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10747786	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10747787	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10783847	0.83[JPT][hapmap]
rs10783850	0.87[JPT][hapmap];0.83[AMR][1000 genomes]
rs10783851	0.87[JPT][hapmap];0.83[AMR][1000 genomes]
rs10783853	1.00[YRI][hapmap]
rs10783854	0.80[CHB][hapmap];0.83[JPT][hapmap];0.89[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs10783855	0.80[CHB][hapmap];0.87[JPT][hapmap];0.90[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs10783856	0.80[CEU][hapmap];0.86[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs10877011	1.00[YRI][hapmap]
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];0.85[YRI][hapmap]
rs10877024	0.83[AMR][1000 genomes]
rs10877025	0.83[AMR][1000 genomes]
rs10877026	0.82[AMR][1000 genomes]
rs10877028	0.87[JPT][hapmap]
rs10877029	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10877030	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10877031	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10877032	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11172333	0.83[JPT][hapmap];1.00[YRI][hapmap]
rs11172335	0.83[JPT][hapmap];1.00[YRI][hapmap]
rs11172344	0.83[JPT][hapmap]
rs11172349	0.83[JPT][hapmap];1.00[YRI][hapmap]
rs11172351	0.83[JPT][hapmap];0.85[YRI][hapmap]
rs11172362	0.81[AMR][1000 genomes]
rs11172367	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]
rs11172368	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11172371	0.82[CHB][hapmap];1.00[YRI][hapmap];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11172375	0.82[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs11172378	0.82[CHB][hapmap];0.80[ASN][1000 genomes]
rs12312955	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12319233	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12426201	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1599750	0.84[AMR][1000 genomes]
rs1599751	0.87[JPT][hapmap];0.84[AMR][1000 genomes]
rs1599931	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1875124	0.83[JPT][hapmap];1.00[YRI][hapmap]
rs1875125	0.94[JPT][hapmap];0.85[YRI][hapmap];0.84[AMR][1000 genomes]
rs1962047	0.82[CHB][hapmap];0.82[ASN][1000 genomes]
rs2002275	0.96[CEU][hapmap];0.82[CHB][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2069502	0.85[YRI][hapmap]
rs2072052	1.00[YRI][hapmap]
rs3751331	0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs3825079	0.83[JPT][hapmap];1.00[YRI][hapmap]
rs4237844	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4646536	0.83[JPT][hapmap]
rs4760171	0.87[JPT][hapmap]
rs4760172	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4760332	0.94[JPT][hapmap];0.85[YRI][hapmap]
rs4760339	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4760340	0.87[CHB][hapmap];0.82[ASN][1000 genomes]
rs4760341	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs5017863	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs59401446	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6581155	0.83[JPT][hapmap]
rs6581157	0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs703842	0.83[JPT][hapmap]
rs7134797	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs724834	0.84[JPT][hapmap];0.85[YRI][hapmap]
rs7312623	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7489290	0.86[JPT][hapmap]
rs7969844	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8181644	0.83[JPT][hapmap]
rs870392	0.94[JPT][hapmap];1.00[YRI][hapmap]
rs871871	0.94[JPT][hapmap]
rs923829	0.84[JPT][hapmap]
rs9645819	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[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:10)

SNP	Gene	Cis/trans	Tissue	Source
rs11172369	XRCC6BP1	cis	Muscle Skeletal	GTEx
rs11172369	XRCC6BP1	Cis_1M	lymphoblastoid	RTeQTL
rs11172369	METTL21B	cis	lung	GTEx
rs11172369	XRCC6BP1	cis	Adipose Subcutaneous	GTEx
rs11172369	FAM119B	cis	Lymphoblastoid	GTEx
rs11172369	XRCC6BP1	cis	Whole Blood	GTEx
rs11172369	XRCC6BP1	cis	Artery Tibial	GTEx
rs11172369	XRCC6BP1	cis	Heart Left Ventricle	GTEx
rs11172369	TSFM	Cis_1M	lymphoblastoid	RTeQTL
rs11172369	XRCC6BP1	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:58270400-58280600	Weak transcription	Colonic Mucosa	Colon
2	chr12:58275400-58281600	Weak transcription	Esophagus	oesophagus
3	chr12:58275800-58280800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr12:58276000-58281600	Weak transcription	Hela-S3	cervix
5	chr12:58276000-58281800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr12:58277600-58280800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr12:58279800-58281800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr12:58279800-58283000	Enhancers	Fetal Lung	lung
9	chr12:58279800-58287000	Enhancers	Fetal Stomach	stomach
10	chr12:58280000-58280600	Weak transcription	Stomach Mucosa	stomach
11	chr12:58280200-58281200	Weak transcription	NH-A	brain
12	chr12:58280200-58281600	Enhancers	Skeletal Muscle Male	skeletal muscle
13	chr12:58280200-58281800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr12:58280200-58287400	Enhancers	Fetal Muscle Leg	muscle
15	chr12:58280400-58280600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr12:58280400-58280600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
17	chr12:58280400-58280600	Enhancers	Brain Hippocampus Middle	brain
18	chr12:58280400-58280800	Enhancers	Psoas Muscle	Psoas
19	chr12:58280400-58281000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
20	chr12:58280400-58281000	Enhancers	Fetal Heart	heart
21	chr12:58280400-58281000	Enhancers	Left Ventricle	heart
22	chr12:58280400-58281000	Enhancers	Rectal Mucosa Donor 29	rectum
23	chr12:58280400-58281000	Enhancers	Sigmoid Colon	Sigmoid Colon
24	chr12:58280400-58281000	Enhancers	HSMMtube	muscle
25	chr12:58280400-58281600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr12:58280400-58281600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr12:58280400-58281600	Enhancers	Breast Myoepithelial Primary Cells	Breast
28	chr12:58280400-58281600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr12:58280400-58281600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr12:58280400-58281600	Enhancers	NHDF-Ad	bronchial
31	chr12:58280400-58281600	Enhancers	NHLF	lung
32	chr12:58280400-58281800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr12:58280400-58281800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr12:58280400-58281800	Enhancers	Skeletal Muscle Female	skeletal muscle
35	chr12:58280400-58281800	Enhancers	HMEC	breast
36	chr12:58280400-58282000	Enhancers	Ovary	ovary
37	chr12:58280400-58282000	Enhancers	Rectal Mucosa Donor 31	rectum
38	chr12:58280400-58284400	Enhancers	Right Atrium	heart
39	chr12:58280400-58284800	Enhancers	Lung	lung
40	chr12:58280400-58288000	Enhancers	Fetal Intestine Large	intestine

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