Variant report

Variant	rs10877022
Chromosome Location	chr12:58223937-58223938
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:58217743..58220104-chr12:58222008..58224494,2	MCF-7	breast:
2	chr12:58218535..58220523-chr12:58222880..58224447,2	K562	blood:

Variant related genes	Relation type
ENSG00000207789	Chromatin interaction
ENSG00000175215	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10431505	0.82[AFR][1000 genomes]
rs10783847	0.85[AFR][1000 genomes]
rs10783848	0.83[AFR][1000 genomes]
rs10783850	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10783851	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10783854	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10783855	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10783856	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs10877024	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10877025	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10877026	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10877029	0.81[AMR][1000 genomes]
rs10877030	0.81[AMR][1000 genomes]
rs11172344	0.83[AFR][1000 genomes]
rs11172361	0.81[EUR][1000 genomes]
rs11172362	0.81[EUR][1000 genomes]
rs1599750	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1599751	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1875125	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4760171	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4760172	0.81[AMR][1000 genomes]
rs4760332	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4760333	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4760335	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7489290	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs870392	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs871871	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[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:12)

SNP	Gene	Cis/trans	Tissue	Source
rs10877022	XRCC6BP1	cis	Heart Left Ventricle	GTEx
rs10877022	XRCC6BP1	cis	Muscle Skeletal	GTEx
rs10877022	XRCC6BP1	cis	Whole Blood	GTEx
rs10877022	METTL21B	cis	Esophagus Muscularis	GTEx
rs10877022	XRCC6BP1	cis	lung	GTEx
rs10877022	METTL21B	cis	Muscle Skeletal	GTEx
rs10877022	XRCC6BP1	cis	Artery Tibial	GTEx
rs10877022	XRCC6BP1	cis	Skin Sun Exposed Lower leg	GTEx
rs10877022	METTL21B	cis	Whole Blood	GTEx
rs10877022	TSFM	Cis_1M	lymphoblastoid	RTeQTL
rs10877022	FAM119B	Cis_1M	lymphoblastoid	RTeQTL
rs10877022	XRCC6BP1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:58209400-58226800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr12:58211400-58224600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr12:58211400-58224800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr12:58211600-58224000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr12:58212000-58224400	Strong transcription	Fetal Intestine Large	intestine
6	chr12:58212000-58224800	Strong transcription	Thymus	Thymus
7	chr12:58212200-58224800	Strong transcription	Brain Germinal Matrix	brain
8	chr12:58212600-58224000	Strong transcription	Fetal Lung	lung
9	chr12:58212600-58224200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr12:58213400-58224000	Strong transcription	Cortex derived primary cultured neurospheres	brain
11	chr12:58213600-58224000	Strong transcription	HUES48 Cell Line	embryonic stem cell
12	chr12:58213600-58224400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
13	chr12:58213800-58224000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr12:58214400-58224000	Strong transcription	Dnd41	blood
15	chr12:58215400-58227200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr12:58217200-58224400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr12:58217400-58225400	Strong transcription	HepG2	liver
18	chr12:58220600-58225600	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
19	chr12:58221000-58224600	Strong transcription	K562	blood
20	chr12:58221400-58224800	Strong transcription	Fetal Muscle Trunk	muscle
21	chr12:58222400-58224400	Genic enhancers	Brain Anterior Caudate	brain
22	chr12:58222400-58224600	Genic enhancers	Primary neutrophils fromperipheralblood	blood
23	chr12:58222600-58224000	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
24	chr12:58222600-58224000	Genic enhancers	Primary T helper cells PMA-I stimulated	--
25	chr12:58222600-58225400	Weak transcription	NHEK	skin
26	chr12:58222800-58224400	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr12:58222800-58224600	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr12:58222800-58224800	Genic enhancers	Primary B cells from peripheral blood	blood
29	chr12:58222800-58224800	Genic enhancers	Lung	lung
30	chr12:58222800-58225400	Weak transcription	HSMMtube	muscle
31	chr12:58222800-58230200	Enhancers	Right Atrium	heart
32	chr12:58222800-58230400	Genic enhancers	Fetal Stomach	stomach
33	chr12:58223000-58224000	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr12:58223000-58224000	Enhancers	Fetal Heart	heart
35	chr12:58223000-58224400	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr12:58223000-58224400	Weak transcription	Stomach Mucosa	stomach
37	chr12:58223000-58224400	Genic enhancers	Spleen	Spleen
38	chr12:58223000-58224600	Genic enhancers	Primary T cells fromperipheralblood	blood
39	chr12:58223000-58225000	Weak transcription	Small Intestine	intestine
40	chr12:58223000-58225200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
41	chr12:58223000-58225400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
42	chr12:58223000-58225400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
43	chr12:58223000-58228400	Genic enhancers	Fetal Thymus	thymus
44	chr12:58223000-58230400	Genic enhancers	Fetal Muscle Leg	muscle
45	chr12:58223200-58224000	Genic enhancers	Primary monocytes fromperipheralblood	blood
46	chr12:58223200-58224000	Genic enhancers	Esophagus	oesophagus
47	chr12:58223200-58224000	Genic enhancers	Rectal Mucosa Donor 29	rectum
48	chr12:58223200-58224400	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr12:58223200-58225200	Enhancers	Primary T helper naive cells from peripheral blood	blood
50	chr12:58223200-58225400	Enhancers	Primary T killer memory cells from peripheral blood	blood

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