Variant report

Variant	rs11172372
Chromosome Location	chr12:58286273-58286274
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:58235372..58242263-chr12:58281059..58286678,18	MCF-7	breast:
2	chr12:58271722..58273746-chr12:58285957..58287603,2	MCF-7	breast:
3	chr12:58238932..58241410-chr12:58284521..58286347,2	K562	blood:
4	chr12:58282465..58284033-chr12:58284765..58286561,2	MCF-7	breast:
5	chr12:58233944..58243826-chr12:58273095..58290464,46	MCF-7	breast:
6	chr12:58245905..58248247-chr12:58284450..58287100,2	MCF-7	breast:
7	chr12:58281679..58287586-chr12:58288167..58292013,9	MCF-7	breast:

Variant related genes	Relation type
ENSG00000245651	Chromatin interaction
ENSG00000175215	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10877033	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10877034	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11172371	0.88[CHB][hapmap];0.83[JPT][hapmap];0.83[ASN][1000 genomes]
rs11172375	0.80[ASN][1000 genomes]
rs11172378	0.88[CHB][hapmap];0.81[JPT][hapmap];0.82[ASN][1000 genomes]
rs1962047	0.88[CHB][hapmap];0.81[JPT][hapmap];0.82[ASN][1000 genomes]
rs2002275	0.88[CHB][hapmap];0.82[ASN][1000 genomes]
rs3751330	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3751331	0.82[ASN][1000 genomes]
rs4128707	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4237845	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4417327	0.96[ASN][1000 genomes]
rs4553410	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4630335	0.83[CHB][hapmap]
rs4760340	0.81[CHB][hapmap];0.82[ASN][1000 genomes]
rs6581157	0.83[ASN][1000 genomes]
rs6581159	0.81[JPT][hapmap]
rs6650217	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6650218	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6650219	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7954591	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7954957	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7963992	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7971877	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[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
rs11172372	XRCC6BP1	Cis_1M	lymphoblastoid	RTeQTL
rs11172372	XRCC6BP1	cis	Adipose Subcutaneous	GTEx
rs11172372	XRCC6BP1	cis	Muscle Skeletal	GTEx
rs11172372	XRCC6BP1	cis	Skin Sun Exposed Lower leg	GTEx
rs11172372	XRCC6BP1	cis	Whole Blood	GTEx
rs11172372	XRCC6BP1	cis	Heart Left Ventricle	GTEx
rs11172372	XRCC6BP1	cis	Thyroid	GTEx
rs11172372	XRCC6BP1	cis	lung	GTEx
rs11172372	XRCC6BP1	cis	Artery Tibial	GTEx
rs11172372	XRCC6BP1	cis	Esophagus Mucosa	GTEx

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:58279800-58287000	Enhancers	Fetal Stomach	stomach
2	chr12:58280200-58287400	Enhancers	Fetal Muscle Leg	muscle
3	chr12:58280400-58288000	Enhancers	Fetal Intestine Large	intestine
4	chr12:58281000-58288000	Enhancers	Fetal Muscle Trunk	muscle
5	chr12:58281400-58287800	Enhancers	Cortex derived primary cultured neurospheres	brain
6	chr12:58281400-58287800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
7	chr12:58281600-58287200	Enhancers	Fetal Intestine Small	intestine
8	chr12:58281600-58288400	Enhancers	K562	blood
9	chr12:58282200-58289600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr12:58282400-58287800	Enhancers	Ovary	ovary
11	chr12:58282800-58287400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr12:58282800-58287400	Weak transcription	Primary hematopoietic stem cells	blood
13	chr12:58282800-58287400	Enhancers	Fetal Kidney	kidney
14	chr12:58283000-58286400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr12:58283000-58287000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr12:58283000-58287000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr12:58283000-58287800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr12:58283000-58288200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
19	chr12:58283000-58288200	Weak transcription	Primary T helper cells PMA-I stimulated	--
20	chr12:58283200-58287400	Weak transcription	HUES48 Cell Line	embryonic stem cell
21	chr12:58283200-58287400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
22	chr12:58283200-58287600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
23	chr12:58283200-58287600	Weak transcription	Primary T helper cells fromperipheralblood	blood
24	chr12:58283200-58288400	Weak transcription	Primary T cells from cord blood	blood
25	chr12:58283200-58288400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
26	chr12:58283400-58287000	Enhancers	NHDF-Ad	bronchial
27	chr12:58283400-58287200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr12:58283400-58287200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
29	chr12:58283400-58287200	Weak transcription	Fetal Brain Male	brain
30	chr12:58283400-58287400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr12:58283400-58287600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
32	chr12:58283400-58287600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
33	chr12:58283400-58288400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
34	chr12:58283600-58287000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr12:58283600-58287200	Weak transcription	HUES6 Cell Line	embryonic stem cell
36	chr12:58283600-58287200	Weak transcription	HUES64 Cell Line	embryonic stem cell
37	chr12:58283600-58287200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr12:58283600-58287200	Weak transcription	HUVEC	blood vessel
39	chr12:58283600-58287200	Enhancers	Osteobl	bone
40	chr12:58283600-58287400	Weak transcription	Thymus	Thymus
41	chr12:58283600-58287600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
42	chr12:58283800-58286600	Enhancers	Fetal Lung	lung
43	chr12:58283800-58287200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr12:58283800-58287400	Enhancers	Skeletal Muscle Female	skeletal muscle
45	chr12:58284000-58286400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr12:58284000-58286600	Weak transcription	Placenta Amnion	Placenta Amnion
47	chr12:58284200-58286400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr12:58284200-58286600	Weak transcription	Fetal Brain Female	brain
49	chr12:58284200-58287000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr12:58284200-58287000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin

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