Variant report

Variant	rs10783853
Chromosome Location	chr12:58234262-58234263
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:58234242..58236619-chr12:58259394..58262193,2	MCF-7	breast:
2	chr12:58231689..58234671-chr12:58290151..58292853,2	K562	blood:
3	chr12:58233748..58235747-chr12:58295225..58296779,2	MCF-7	breast:
4	chr12:58233992..58236447-chr12:58297834..58300424,2	K562	blood:
5	chr12:58231520..58234671-chr12:58290151..58292853,3	K562	blood:
6	chr12:58233944..58243826-chr12:58273095..58290464,46	MCF-7	breast:

Variant related genes	Relation type
ENSG00000245651	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 15 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10783850	1.00[LWK][hapmap]
rs10783851	1.00[LWK][hapmap]
rs10783852	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10783855	0.81[TSI][hapmap]
rs10877011	1.00[YRI][hapmap]
rs10877019	1.00[LWK][hapmap];0.85[YRI][hapmap]
rs10877028	0.81[TSI][hapmap]
rs11172333	1.00[LWK][hapmap];1.00[YRI][hapmap]
rs11172335	1.00[LWK][hapmap];1.00[YRI][hapmap]
rs11172343	0.85[YRI][hapmap]
rs11172349	1.00[LWK][hapmap];1.00[YRI][hapmap]
rs11172351	1.00[LWK][hapmap];0.85[YRI][hapmap]
rs11172369	1.00[YRI][hapmap]
rs11172371	1.00[YRI][hapmap]
rs1599751	0.81[TSI][hapmap]
rs1599931	1.00[YRI][hapmap]
rs1875124	1.00[LWK][hapmap];1.00[YRI][hapmap]
rs1875125	1.00[YRI][hapmap];0.88[AFR][1000 genomes]
rs2002275	1.00[ASW][hapmap]
rs2069502	1.00[LWK][hapmap];0.85[YRI][hapmap]
rs2072052	1.00[LWK][hapmap];1.00[YRI][hapmap]
rs3825079	1.00[LWK][hapmap];1.00[YRI][hapmap]
rs4237844	0.85[YRI][hapmap]
rs4760332	0.86[ASW][hapmap];1.00[LWK][hapmap];0.85[YRI][hapmap];0.81[AFR][1000 genomes]
rs4760341	0.82[CEU][hapmap];0.85[YRI][hapmap]
rs724834	1.00[YRI][hapmap]
rs7489290	0.92[JPT][hapmap]
rs870392	0.86[ASW][hapmap];1.00[LWK][hapmap];1.00[YRI][hapmap];0.88[AFR][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:15)

SNP	Gene	Cis/trans	Tissue	Source
rs10783853	XRCC6BP1	Cis_1M	lymphoblastoid	RTeQTL
rs10783853	FAM119B	cis	Lymphoblastoid	GTEx
rs10783853	XRCC6BP1	cis	Heart Left Ventricle	GTEx
rs10783853	XRCC6BP1	cis	lung	GTEx
rs10783853	XRCC6BP1	cis	Artery Tibial	GTEx
rs10783853	FAM119B	cis	Cerebellum	GTEx
rs10783853	XRCC6BP1	cis	Adipose Subcutaneous	GTEx
rs10783853	XRCC6BP1	cis	Thyroid	GTEx
rs10783853	FAM119B	cis	Frontal Cortex	GTEx
rs10783853	XRCC6BP1	cis	Whole Blood	GTEx
rs10783853	XRCC6BP1	cis	Nerve Tibial	GTEx
rs10783853	XRCC6BP1	cis	Muscle Skeletal	GTEx
rs10783853	FAM119B	Cis_1M	lymphoblastoid	RTeQTL
rs10783853	TSFM	Cis_1M	lymphoblastoid	RTeQTL
rs10783853	XRCC6BP1	cis	Skin Sun Exposed Lower leg	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:58223400-58236400	Enhancers	Right Ventricle	heart
2	chr12:58224200-58238200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
3	chr12:58224400-58238000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr12:58224400-58238200	Enhancers	Spleen	Spleen
5	chr12:58225200-58237000	Enhancers	Cortex derived primary cultured neurospheres	brain
6	chr12:58225400-58235600	Genic enhancers	Fetal Intestine Small	intestine
7	chr12:58225600-58238200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
8	chr12:58225800-58236000	Enhancers	Brain Angular Gyrus	brain
9	chr12:58226400-58236200	Enhancers	Left Ventricle	heart
10	chr12:58226600-58234600	Enhancers	Esophagus	oesophagus
11	chr12:58226600-58235600	Enhancers	Lung	lung
12	chr12:58226600-58236200	Enhancers	H1 Cell Line	embryonic stem cell
13	chr12:58226600-58236200	Enhancers	Psoas Muscle	Psoas
14	chr12:58226600-58236400	Enhancers	Pancreas	Pancrea
15	chr12:58226800-58237800	Enhancers	Primary monocytes fromperipheralblood	blood
16	chr12:58227000-58236400	Enhancers	Gastric	stomach
17	chr12:58227200-58238200	Enhancers	Small Intestine	intestine
18	chr12:58229200-58238400	Flanking Active TSS	Stomach Smooth Muscle	stomach
19	chr12:58229600-58236600	Enhancers	Stomach Mucosa	stomach
20	chr12:58229800-58236800	Enhancers	HSMM	muscle
21	chr12:58230600-58235400	Enhancers	Primary T killer memory cells from peripheral blood	blood
22	chr12:58230600-58236200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
23	chr12:58230600-58236400	Enhancers	Primary B cells from peripheral blood	blood
24	chr12:58230600-58236600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
25	chr12:58230800-58236200	Enhancers	ES-I3 Cell Line	embryonic stem cell
26	chr12:58231000-58235200	Enhancers	Primary T helper cells fromperipheralblood	blood
27	chr12:58231000-58236000	Enhancers	iPS-20b Cell Line	embryonic stem cell
28	chr12:58231000-58236000	Enhancers	Right Atrium	heart
29	chr12:58231000-58236200	Enhancers	HUES48 Cell Line	embryonic stem cell
30	chr12:58231000-58236400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr12:58231000-58237600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr12:58231200-58235800	Enhancers	iPS-18 Cell Line	embryonic stem cell
33	chr12:58231200-58236200	Enhancers	HUES6 Cell Line	embryonic stem cell
34	chr12:58231200-58236200	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr12:58231200-58236200	Enhancers	iPS-15b Cell Line	embryonic stem cell
36	chr12:58231200-58236400	Enhancers	Liver	Liver
37	chr12:58231600-58234400	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
38	chr12:58231600-58235400	Genic enhancers	Placenta	Placenta
39	chr12:58231600-58236200	Genic enhancers	Fetal Thymus	thymus
40	chr12:58231800-58234800	Weak transcription	HSMMtube	muscle
41	chr12:58231800-58236200	Genic enhancers	Fetal Stomach	stomach
42	chr12:58231800-58237400	Enhancers	Primary neutrophils fromperipheralblood	blood
43	chr12:58232000-58234400	Genic enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr12:58232000-58235800	Enhancers	Primary hematopoietic stem cells	blood
45	chr12:58232000-58236000	Genic enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr12:58232200-58235000	Genic enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr12:58232400-58234600	Enhancers	NHDF-Ad	bronchial
48	chr12:58232400-58236000	Enhancers	Osteobl	bone
49	chr12:58232400-58236200	Genic enhancers	Fetal Muscle Leg	muscle
50	chr12:58232600-58234400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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