Variant report

Variant	rs5017863
Chromosome Location	chr12:58261661-58261662
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:58237087..58244044-chr12:58260690..58267738,8	K562	blood:
2	chr12:58258786..58263861-chr12:58273729..58277386,6	MCF-7	breast:
3	chr12:58240344..58242191-chr12:58260690..58262318,2	K562	blood:
4	chr12:58259629..58265686-chr12:58266089..58272179,8	K562	blood:
5	chr12:58234242..58236619-chr12:58259394..58262193,2	MCF-7	breast:
6	chr12:58257740..58261779-chr12:58273700..58278459,4	MCF-7	breast:
7	chr12:58259698..58262580-chr5:154319260..154321205,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000082515	Chromatin interaction
ENSG00000175215	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10444569	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10747784	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10747786	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10747787	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10783850	0.86[AMR][1000 genomes]
rs10783851	0.86[AMR][1000 genomes]
rs10783854	0.92[AMR][1000 genomes]
rs10783855	0.93[AMR][1000 genomes]
rs10783856	0.90[AMR][1000 genomes]
rs10877024	0.86[AMR][1000 genomes]
rs10877025	0.86[AMR][1000 genomes]
rs10877026	0.85[AMR][1000 genomes]
rs10877029	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10877030	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10877031	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10877032	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11172362	0.84[AMR][1000 genomes]
rs11172367	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11172368	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11172369	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11172371	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12312955	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12319233	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12426201	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1599750	0.87[AMR][1000 genomes]
rs1599751	0.87[AMR][1000 genomes]
rs1599931	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1875125	0.87[AMR][1000 genomes]
rs2002275	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4237844	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4760172	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4760332	0.83[AMR][1000 genomes]
rs4760335	0.80[AMR][1000 genomes]
rs4760339	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4760341	0.89[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs59401446	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7134797	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7312623	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7969844	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs870392	0.83[AMR][1000 genomes]
rs9645819	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[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:9)

SNP	Gene	Cis/trans	Tissue	Source
rs5017863	METTL21B	cis	lung	GTEx
rs5017863	XRCC6BP1	cis	Skin Sun Exposed Lower leg	GTEx
rs5017863	XRCC6BP1	Cis_1M	lymphoblastoid	RTeQTL
rs5017863	XRCC6BP1	cis	Whole Blood	GTEx
rs5017863	XRCC6BP1	cis	Muscle Skeletal	GTEx
rs5017863	TSFM	Cis_1M	lymphoblastoid	RTeQTL
rs5017863	XRCC6BP1	cis	Artery Tibial	GTEx
rs5017863	XRCC6BP1	cis	Adipose Subcutaneous	GTEx
rs5017863	XRCC6BP1	cis	Heart Left Ventricle	GTEx

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:58256400-58264600	Weak transcription	Spleen	Spleen
2	chr12:58258600-58261800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr12:58258600-58262000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr12:58258600-58262200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr12:58259400-58269600	Weak transcription	Aorta	Aorta
6	chr12:58259600-58261800	Weak transcription	Fetal Stomach	stomach
7	chr12:58259600-58262000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr12:58259600-58262000	Weak transcription	Brain Germinal Matrix	brain
9	chr12:58259600-58262000	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr12:58259600-58262000	Weak transcription	Brain Substantia Nigra	brain
11	chr12:58259600-58262200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr12:58259600-58262200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr12:58259600-58262200	Weak transcription	Esophagus	oesophagus
14	chr12:58259600-58262400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr12:58259600-58262600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr12:58259600-58262600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr12:58259600-58262600	Weak transcription	Lung	lung
18	chr12:58259600-58262600	Weak transcription	Pancreas	Pancrea
19	chr12:58259600-58262600	Weak transcription	Psoas Muscle	Psoas
20	chr12:58259600-58262800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr12:58259600-58264000	Enhancers	Placenta	Placenta
22	chr12:58259600-58267800	Weak transcription	Colonic Mucosa	Colon
23	chr12:58259600-58268000	Weak transcription	Left Ventricle	heart
24	chr12:58259800-58261800	Weak transcription	Brain Cingulate Gyrus	brain
25	chr12:58259800-58261800	Weak transcription	Rectal Smooth Muscle	rectum
26	chr12:58259800-58262000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr12:58259800-58262000	Weak transcription	Brain Angular Gyrus	brain
28	chr12:58259800-58262000	Weak transcription	Brain Anterior Caudate	brain
29	chr12:58259800-58262000	Weak transcription	Brain Hippocampus Middle	brain
30	chr12:58259800-58262000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
31	chr12:58259800-58262000	Weak transcription	Duodenum Mucosa	Duodenum
32	chr12:58259800-58262000	Weak transcription	Fetal Heart	heart
33	chr12:58259800-58262000	Weak transcription	Fetal Kidney	kidney
34	chr12:58259800-58262200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr12:58259800-58262200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr12:58259800-58262200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
37	chr12:58259800-58262200	Weak transcription	HSMMtube	muscle
38	chr12:58259800-58262400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr12:58259800-58262600	Weak transcription	HSMM	muscle
40	chr12:58259800-58267600	Weak transcription	Rectal Mucosa Donor 29	rectum
41	chr12:58260000-58261800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr12:58260000-58261800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr12:58260000-58261800	Weak transcription	Colon Smooth Muscle	Colon
44	chr12:58260000-58261800	Weak transcription	Fetal Brain Male	brain
45	chr12:58260000-58261800	Weak transcription	Fetal Lung	lung
46	chr12:58260000-58262000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr12:58260000-58262000	Weak transcription	Duodenum Smooth Muscle	Duodenum
48	chr12:58260000-58262000	Weak transcription	Fetal Muscle Leg	muscle
49	chr12:58260000-58262000	Weak transcription	NHDF-Ad	bronchial
50	chr12:58260000-58262200	Weak transcription	Adipose Nuclei	Adipose

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