Variant report

Variant	rs61935769
Chromosome Location	chr12:58294344-58294345
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:58257612..58259236-chr12:58293224..58296608,3	MCF-7	breast:
2	chr12:58236196..58241196-chr12:58294118..58300852,8	MCF-7	breast:
3	chr12:58225758..58227356-chr12:58293010..58294775,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000175215	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs11172371	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs11172375	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11172378	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1962047	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2002275	0.81[AMR][1000 genomes]
rs3751331	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4628718	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4630335	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6581157	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7306124	0.83[EUR][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:13)

SNP	Gene	Cis/trans	Tissue	Source
rs61935769	XRCC6BP1	cis	lung	GTEx
rs61935769	XRCC6BP1	cis	Whole Blood	GTEx
rs61935769	XRCC6BP1	cis	Esophagus Muscularis	GTEx
rs61935769	XRCC6BP1	cis	Heart Left Ventricle	GTEx
rs61935769	XRCC6BP1	cis	Esophagus Mucosa	GTEx
rs61935769	XRCC6BP1	cis	Artery Tibial	GTEx
rs61935769	XRCC6BP1	Cis_1M	lymphoblastoid	RTeQTL
rs61935769	XRCC6BP1	cis	Thyroid	GTEx
rs61935769	XRCC6BP1	cis	Artery Aorta	GTEx
rs61935769	XRCC6BP1	cis	Muscle Skeletal	GTEx
rs61935769	XRCC6BP1	cis	Nerve Tibial	GTEx
rs61935769	XRCC6BP1	cis	Skin Sun Exposed Lower leg	GTEx
rs61935769	XRCC6BP1	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:58291000-58294400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
2	chr12:58291000-58294400	Enhancers	Primary T cells fromperipheralblood	blood
3	chr12:58292800-58298800	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr12:58292800-58299000	Weak transcription	Fetal Kidney	kidney
5	chr12:58292800-58299000	Weak transcription	Rectal Mucosa Donor 29	rectum
6	chr12:58293200-58294400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
7	chr12:58293200-58295800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr12:58293200-58295800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr12:58293200-58295800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr12:58293200-58296000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr12:58293200-58296000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr12:58293200-58296200	Weak transcription	Cortex derived primary cultured neurospheres	brain
13	chr12:58293200-58296600	Weak transcription	Pancreas	Pancrea
14	chr12:58293200-58298000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr12:58293200-58298800	Weak transcription	Adipose Nuclei	Adipose
16	chr12:58293200-58298800	Weak transcription	Placenta	Placenta
17	chr12:58293200-58299000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr12:58293200-58299000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
19	chr12:58293200-58299000	Weak transcription	Brain Hippocampus Middle	brain
20	chr12:58293200-58299000	Weak transcription	Brain Inferior Temporal Lobe	brain
21	chr12:58293200-58299000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr12:58293200-58299000	Weak transcription	Brain Substantia Nigra	brain
23	chr12:58293200-58299000	Weak transcription	Fetal Lung	lung
24	chr12:58293200-58299000	Weak transcription	A549	lung
25	chr12:58293200-58299000	Weak transcription	NHDF-Ad	bronchial
26	chr12:58293400-58295600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr12:58293400-58296200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr12:58293400-58296200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr12:58293400-58296200	Weak transcription	Aorta	Aorta
30	chr12:58293400-58296200	Weak transcription	Stomach Smooth Muscle	stomach
31	chr12:58293400-58296400	Weak transcription	Osteobl	bone
32	chr12:58293400-58296600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr12:58293400-58298800	Weak transcription	Hela-S3	cervix
34	chr12:58293400-58299000	Weak transcription	Muscle Satellite Cultured Cells	--
35	chr12:58293400-58299000	Weak transcription	Brain Anterior Caudate	brain
36	chr12:58293400-58299000	Weak transcription	Colon Smooth Muscle	Colon
37	chr12:58293400-58299000	Weak transcription	Fetal Stomach	stomach
38	chr12:58293400-58299000	Weak transcription	K562	blood
39	chr12:58293800-58294600	Enhancers	GM12878-XiMat	blood
40	chr12:58293800-58298800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr12:58293800-58299000	Weak transcription	Primary T cells from cord blood	blood
42	chr12:58293800-58299000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
43	chr12:58293800-58299000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
44	chr12:58293800-58299000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
45	chr12:58293800-58299000	Weak transcription	Duodenum Mucosa	Duodenum
46	chr12:58293800-58299000	Weak transcription	Skeletal Muscle Male	skeletal muscle
47	chr12:58293800-58299000	Weak transcription	HMEC	breast
48	chr12:58294000-58299000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr12:58294000-58299000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
50	chr12:58294000-58299000	Weak transcription	Primary T helper cells PMA-I stimulated	--

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