Variant report

Variant	rs11172389
Chromosome Location	chr12:58337671-58337672
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:58335319..58338203-chr12:58340129..58346317,10	K562	blood:
2	chr12:58334273..58337039-chr12:58337330..58340023,3	K562	blood:
3	chr12:58336001..58339574-chr12:58342620..58345484,3	MCF-7	breast:
4	chr12:58336020..58338569-chr12:58461127..58463440,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000166896	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 14 )

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

rs_ID	r²[population]
rs10431506	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10747788	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10783857	0.86[AMR][1000 genomes]
rs10783858	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10783860	0.80[AFR][1000 genomes]
rs10877039	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10877040	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10877041	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11172387	0.80[EUR][1000 genomes]
rs11172388	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2372309	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3751325	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3751326	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3751327	0.90[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs4373979	0.80[EUR][1000 genomes]
rs4509811	0.80[EUR][1000 genomes]
rs4534624	0.80[EUR][1000 genomes]
rs4590915	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4760174	0.80[EUR][1000 genomes]
rs4760344	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7136981	0.80[EUR][1000 genomes]
rs7298370	0.80[EUR][1000 genomes]
rs7358584	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9971803	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[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:14)

SNP	Gene	Cis/trans	Tissue	Source
rs11172389	XRCC6BP1	Cis_1M	lymphoblastoid	RTeQTL
rs11172389	XRCC6BP1	cis	Nerve Tibial	GTEx
rs11172389	XRCC6BP1	cis	Heart Left Ventricle	GTEx
rs11172389	XRCC6BP1	cis	Esophagus Muscularis	GTEx
rs11172389	XRCC6BP1	cis	Muscle Skeletal	GTEx
rs11172389	XRCC6BP1	cis	Artery Tibial	GTEx
rs11172389	XRCC6BP1	cis	Stomach	GTEx
rs11172389	XRCC6BP1	cis	Adipose Subcutaneous	GTEx
rs11172389	XRCC6BP1	cis	Thyroid	GTEx
rs11172389	XRCC6BP1	cis	Whole Blood	GTEx
rs11172389	XRCC6BP1	cis	Esophagus Mucosa	GTEx
rs11172389	XRCC6BP1	cis	Skin Sun Exposed Lower leg	GTEx
rs11172389	XRCC6BP1	cis	lung	GTEx
rs11172389	XRCC6BP1	cis	Artery Aorta	GTEx

Chromatin state (count:92 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:58335800-58343000	Weak transcription	Ovary	ovary
2	chr12:58336000-58344800	Weak transcription	Left Ventricle	heart
3	chr12:58336000-58345200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr12:58336000-58347600	Weak transcription	Esophagus	oesophagus
5	chr12:58336000-58348400	Weak transcription	Gastric	stomach
6	chr12:58336000-58348600	Weak transcription	Aorta	Aorta
7	chr12:58336000-58348600	Weak transcription	Lung	lung
8	chr12:58336000-58351000	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr12:58336000-58351000	Weak transcription	Colon Smooth Muscle	Colon
10	chr12:58336000-58351200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr12:58336000-58351200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr12:58336000-58351200	Weak transcription	Spleen	Spleen
13	chr12:58336000-58353000	Weak transcription	Small Intestine	intestine
14	chr12:58336200-58337800	Enhancers	Primary monocytes fromperipheralblood	blood
15	chr12:58336200-58337800	Enhancers	Primary hematopoietic stem cells	blood
16	chr12:58336200-58338200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
17	chr12:58336200-58338400	Enhancers	Fetal Thymus	thymus
18	chr12:58336200-58339600	Weak transcription	Fetal Stomach	stomach
19	chr12:58336200-58340800	Weak transcription	Stomach Smooth Muscle	stomach
20	chr12:58336200-58344800	Weak transcription	Duodenum Mucosa	Duodenum
21	chr12:58336200-58345000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr12:58336200-58346600	Weak transcription	HUES48 Cell Line	embryonic stem cell
23	chr12:58336200-58346600	Weak transcription	Fetal Muscle Leg	muscle
24	chr12:58336200-58347600	Weak transcription	HUES6 Cell Line	embryonic stem cell
25	chr12:58336200-58350600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr12:58336200-58350600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr12:58336200-58350800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr12:58336200-58351000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr12:58336200-58351000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
30	chr12:58336200-58351000	Weak transcription	Skeletal Muscle Male	skeletal muscle
31	chr12:58336200-58351200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr12:58336200-58351200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr12:58336200-58351200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr12:58336200-58351200	Weak transcription	Fetal Intestine Small	intestine
35	chr12:58336200-58351200	Weak transcription	Placenta	Placenta
36	chr12:58336200-58351400	Weak transcription	Brain Anterior Caudate	brain
37	chr12:58336200-58351400	Weak transcription	Fetal Lung	lung
38	chr12:58336200-58351600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
39	chr12:58336200-58351600	Weak transcription	HUVEC	blood vessel
40	chr12:58336200-58353000	Weak transcription	Stomach Mucosa	stomach
41	chr12:58336200-58353400	Weak transcription	Fetal Kidney	kidney
42	chr12:58336200-58353600	Weak transcription	Brain Substantia Nigra	brain
43	chr12:58336200-58353600	Weak transcription	Placenta Amnion	Placenta Amnion
44	chr12:58336200-58353800	Weak transcription	Brain Angular Gyrus	brain
45	chr12:58336200-58353800	Weak transcription	Brain Hippocampus Middle	brain
46	chr12:58336200-58354000	Weak transcription	HUES64 Cell Line	embryonic stem cell
47	chr12:58336200-58354000	Weak transcription	Muscle Satellite Cultured Cells	--
48	chr12:58336200-58354000	Weak transcription	Psoas Muscle	Psoas
49	chr12:58336200-58356200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
50	chr12:58336200-58359600	Weak transcription	A549	lung

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