Variant report

Variant	rs10783854
Chromosome Location	chr12:58244630-58244631
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SPI1	chr12:58244606-58244996	GM12891	blood:	n/a	n/a
2	SPI1	chr12:58244479-58245111	GM12878	blood:	n/a	n/a
3	SPI1	chr12:58244593-58245014	GM12891	blood:	n/a	n/a
4	ZNF384	chr12:58244571-58244988	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:58242941..58244963-chr12:58268081..58270017,2	MCF-7	breast:
2	chr12:58242304..58245616-chr12:58249700..58252095,4	MCF-7	breast:
3	chr12:58243942..58248184-chr12:58281468..58284195,4	MCF-7	breast:

Variant related genes	Relation type
CTDSP2	TF binding region

Extended variants
information (count: 50 )
Associated
traits (count: 16 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10444569	0.91[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs10747784	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10747786	0.87[JPT][hapmap];0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs10747787	0.87[JPT][hapmap];0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs10783850	0.87[CEU][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10783851	0.87[CEU][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10783855	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10783856	0.96[CEU][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10877022	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10877024	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10877025	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10877026	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10877028	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs10877029	0.87[CEU][hapmap];0.87[JPT][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10877030	0.87[CEU][hapmap];0.87[JPT][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10877031	0.91[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs10877032	0.85[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs11172361	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11172362	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11172367	0.87[JPT][hapmap];0.85[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs11172368	0.83[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs11172369	0.80[CHB][hapmap];0.83[JPT][hapmap];0.89[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs11172371	0.86[AMR][1000 genomes]
rs12312955	0.87[AMR][1000 genomes]
rs12319233	0.88[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs12426201	0.91[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs1599750	1.00[CEU][hapmap];0.87[CHB][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1599751	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1599931	0.88[JPT][hapmap];0.92[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs1875125	0.85[CEU][hapmap];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2002275	0.87[AMR][1000 genomes]
rs4237844	0.87[JPT][hapmap];0.91[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs4760171	0.87[CEU][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4760172	0.87[CEU][hapmap];0.87[JPT][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4760332	0.87[CEU][hapmap];0.82[JPT][hapmap];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4760333	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4760335	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4760339	0.84[CEU][hapmap];0.82[JPT][hapmap];0.91[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs4760341	0.80[CHB][hapmap];0.82[JPT][hapmap];0.87[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs5017863	0.92[AMR][1000 genomes]
rs59401446	0.83[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs7134797	0.84[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs7298479	0.86[EUR][1000 genomes]
rs7312623	0.87[JPT][hapmap];0.91[YRI][hapmap];0.91[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs7489290	0.86[CEU][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7969844	0.80[ASN][1000 genomes]
rs870392	0.87[CEU][hapmap];0.82[JPT][hapmap];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs871871	0.87[CEU][hapmap];0.82[JPT][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9645819	0.82[AMR][1000 genomes];0.80[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:16)

SNP	Gene	Cis/trans	Tissue	Source
rs10783854	FAM119B	cis	Cerebellum	GTEx
rs10783854	FAM119B	cis	Temporal Cortex	GTEx
rs10783854	XRCC6BP1	cis	Adipose Subcutaneous	GTEx
rs10783854	METTL21B	cis	Esophagus Muscularis	GTEx
rs10783854	XRCC6BP1	cis	Skin Sun Exposed Lower leg	GTEx
rs10783854	XRCC6BP1	cis	Heart Left Ventricle	GTEx
rs10783854	XRCC6BP1	cis	Esophagus Muscularis	GTEx
rs10783854	XRCC6BP1	cis	Whole Blood	GTEx
rs10783854	FAM119B	cis	Frontal Cortex	GTEx
rs10783854	XRCC6BP1	cis	lung	GTEx
rs10783854	XRCC6BP1	Cis_1M	lymphoblastoid	RTeQTL
rs10783854	XRCC6BP1	cis	Artery Tibial	GTEx
rs10783854	FAM119B	Cis_1M	lymphoblastoid	RTeQTL
rs10783854	XRCC6BP1	cis	Muscle Skeletal	GTEx
rs10783854	METTL21B	cis	Muscle Skeletal	GTEx
rs10783854	TSFM	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:75 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:58241200-58244800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr12:58241200-58244800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr12:58241200-58244800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr12:58241200-58245000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr12:58241200-58245000	Weak transcription	Fetal Lung	lung
6	chr12:58241200-58245000	Weak transcription	A549	lung
7	chr12:58241200-58245600	Weak transcription	Duodenum Smooth Muscle	Duodenum
8	chr12:58241200-58245600	Weak transcription	NHDF-Ad	bronchial
9	chr12:58241200-58245800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
10	chr12:58241200-58245800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr12:58241200-58246000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr12:58241200-58246000	Weak transcription	Fetal Brain Male	brain
13	chr12:58241200-58246000	Weak transcription	Pancreatic Islets	Pancreatic Islet
14	chr12:58241200-58246000	Weak transcription	HMEC	breast
15	chr12:58241200-58246200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr12:58241400-58244800	Weak transcription	Brain Germinal Matrix	brain
17	chr12:58241400-58244800	Weak transcription	Rectal Smooth Muscle	rectum
18	chr12:58241400-58245800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr12:58241800-58244800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr12:58241800-58245000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
21	chr12:58241800-58245200	Weak transcription	Colonic Mucosa	Colon
22	chr12:58242000-58245000	Weak transcription	Primary T cells from cord blood	blood
23	chr12:58242200-58244800	Weak transcription	HUES6 Cell Line	embryonic stem cell
24	chr12:58242200-58244800	Weak transcription	Lung	lung
25	chr12:58242200-58245000	Weak transcription	Primary T helper cells fromperipheralblood	blood
26	chr12:58242200-58245400	Weak transcription	H9 Cell Line	embryonic stem cell
27	chr12:58242200-58246000	Weak transcription	Esophagus	oesophagus
28	chr12:58242200-58246000	Weak transcription	Pancreas	Pancrea
29	chr12:58242400-58244800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
30	chr12:58242600-58245000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr12:58243000-58245600	Enhancers	Fetal Muscle Leg	muscle
32	chr12:58243000-58246200	Enhancers	Psoas Muscle	Psoas
33	chr12:58243200-58250200	Weak transcription	K562	blood
34	chr12:58243600-58246200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
35	chr12:58244000-58245000	Enhancers	Ovary	ovary
36	chr12:58244000-58246000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr12:58244000-58246000	Enhancers	Adipose Nuclei	Adipose
38	chr12:58244000-58246000	Enhancers	Fetal Muscle Trunk	muscle
39	chr12:58244000-58246200	Enhancers	Primary hematopoietic stem cells short term culture	blood
40	chr12:58244000-58246200	Enhancers	Fetal Thymus	thymus
41	chr12:58244000-58246200	Enhancers	Right Atrium	heart
42	chr12:58244000-58247600	Enhancers	Spleen	Spleen
43	chr12:58244200-58244800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr12:58244200-58245800	Enhancers	Primary B cells from peripheral blood	blood
45	chr12:58244200-58245800	Enhancers	Stomach Smooth Muscle	stomach
46	chr12:58244200-58246200	Enhancers	Placenta	Placenta
47	chr12:58244200-58246200	Enhancers	Thymus	Thymus
48	chr12:58244200-58246400	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
49	chr12:58244400-58244800	Enhancers	Brain Hippocampus Middle	brain
50	chr12:58244400-58245000	Bivalent Enhancer	Monocytes-CD14+_RO01746	blood

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