Variant report

Variant	rs10783859
Chromosome Location	chr12:58332794-58332795
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:58238851..58241260-chr12:58332365..58335429,3	K562	blood:
2	chr12:58297630..58299144-chr12:58332422..58334699,2	K562	blood:
3	chr12:58162992..58165092-chr12:58332637..58335110,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000175215	Chromatin interaction
ENSG00000037897	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 17 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10122	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10431506	0.85[CEU][hapmap]
rs10747788	0.82[CEU][hapmap]
rs10877036	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10877037	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10877040	0.82[CEU][hapmap]
rs11172372	0.81[JPT][hapmap]
rs11172387	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12308413	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2888288	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4272820	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4335583	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4373979	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4509811	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4534624	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4583019	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4760174	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4760343	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4760346	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4760347	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6581159	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7133278	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7136981	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7295748	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7298370	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7299249	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7975227	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7978588	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9971722	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[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:17)

SNP	Gene	Cis/trans	Tissue	Source
rs10783859	XRCC6BP1	cis	Esophagus Muscularis	GTEx
rs10783859	XRCC6BP1	cis	normal skin	skin_eQTL
rs10783859	XRCC6BP1	cis	Thyroid	GTEx
rs10783859	XRCC6BP1	cis	Adipose Subcutaneous	GTEx
rs10783859	XRCC6BP1	cis	Nerve Tibial	GTEx
rs10783859	XRCC6BP1	cis	Heart Left Ventricle	GTEx
rs10783859	XRCC6BP1	cis	Whole Blood	GTEx
rs10783859	XRCC6BP1	cis	Esophagus Mucosa	GTEx
rs10783859	XRCC6BP1	cis	lesional skin	skin_eQTL
rs10783859	XRCC6BP1	cis	Muscle Skeletal	GTEx
rs10783859	XRCC6BP1	Cis_1M	lymphoblastoid	RTeQTL
rs10783859	XRCC6BP1	cis	multi-tissue	Pritchard
rs10783859	XRCC6BP1	cis	lung	GTEx
rs10783859	XRCC6BP1	cis	uninvolved skin	skin_eQTL
rs10783859	XRCC6BP1	cis	Artery Tibial	GTEx
rs10783859	XRCC6BP1	cis	Artery Aorta	GTEx
rs10783859	XRCC6BP1	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:90 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:58330200-58334400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr12:58330200-58334400	Weak transcription	Colonic Mucosa	Colon
3	chr12:58330200-58334400	Weak transcription	Small Intestine	intestine
4	chr12:58330200-58334600	Weak transcription	Esophagus	oesophagus
5	chr12:58330200-58334600	Weak transcription	Left Ventricle	heart
6	chr12:58330200-58334600	Weak transcription	Lung	lung
7	chr12:58330200-58334600	Weak transcription	Pancreas	Pancrea
8	chr12:58330200-58334600	Weak transcription	Spleen	Spleen
9	chr12:58330200-58334800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr12:58330400-58332800	Enhancers	Primary neutrophils fromperipheralblood	blood
11	chr12:58330400-58334600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr12:58330400-58334600	Weak transcription	Placenta	Placenta
13	chr12:58330400-58334600	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr12:58330600-58333400	Weak transcription	Primary hematopoietic stem cells	blood
15	chr12:58330600-58333600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
16	chr12:58330600-58333600	Weak transcription	Primary T helper cells PMA-I stimulated	--
17	chr12:58330600-58333800	Weak transcription	Primary T cells from cord blood	blood
18	chr12:58330600-58333800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
19	chr12:58330600-58334000	Weak transcription	Primary T helper cells fromperipheralblood	blood
20	chr12:58330600-58334000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
21	chr12:58330600-58334000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
22	chr12:58330600-58334200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr12:58330600-58334200	Weak transcription	Primary T cells fromperipheralblood	blood
24	chr12:58330600-58334200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr12:58330600-58334200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr12:58330600-58334200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr12:58330600-58334200	Weak transcription	Brain Anterior Caudate	brain
28	chr12:58330600-58334200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
29	chr12:58330600-58334200	Weak transcription	Rectal Mucosa Donor 31	rectum
30	chr12:58330600-58334200	Weak transcription	Sigmoid Colon	Sigmoid Colon
31	chr12:58330600-58334400	Weak transcription	HUES6 Cell Line	embryonic stem cell
32	chr12:58330600-58334400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr12:58330600-58334400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
34	chr12:58330600-58334400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
35	chr12:58330600-58334400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
36	chr12:58330600-58334400	Weak transcription	Adipose Nuclei	Adipose
37	chr12:58330600-58334400	Weak transcription	Brain Hippocampus Middle	brain
38	chr12:58330600-58334400	Weak transcription	Brain Inferior Temporal Lobe	brain
39	chr12:58330600-58334400	Weak transcription	Colon Smooth Muscle	Colon
40	chr12:58330600-58334400	Weak transcription	Duodenum Mucosa	Duodenum
41	chr12:58330600-58334400	Weak transcription	Duodenum Smooth Muscle	Duodenum
42	chr12:58330600-58334400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
43	chr12:58330600-58334400	Weak transcription	Fetal Intestine Small	intestine
44	chr12:58330600-58334400	Weak transcription	Rectal Mucosa Donor 29	rectum
45	chr12:58330600-58334400	Weak transcription	Skeletal Muscle Male	skeletal muscle
46	chr12:58330600-58334400	Weak transcription	Skeletal Muscle Female	skeletal muscle
47	chr12:58330600-58334400	Weak transcription	Stomach Mucosa	stomach
48	chr12:58330600-58334400	Weak transcription	Stomach Smooth Muscle	stomach
49	chr12:58330600-58334400	Weak transcription	A549	lung
50	chr12:58330600-58334400	Weak transcription	HMEC	breast

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