Variant report

Variant	rs7489290
Chromosome Location	chr12:58228588-58228589
allele	C/G
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	ATF2	chr12:58228183-58228594	GM12878	blood:	n/a	n/a
2	SPI1	chr12:58228254-58228632	GM12891	blood:	n/a	chr12:58228521-58228534
3	RAD21	chr12:58228211-58228599	H1-hESC	embryonic stem cell:	n/a	n/a
4	SPI1	chr12:58228240-58228595	GM12891	blood:	n/a	chr12:58228521-58228534
5	RUNX3	chr12:58228083-58228682	GM12878	blood:	n/a	n/a
6	SPI1	chr12:58228086-58228663	GM12878	blood:	n/a	chr12:58228521-58228534
7	SPI1	chr12:58228196-58228599	GM12878	blood:	n/a	chr12:58228521-58228534
8	RUNX3	chr12:58228169-58228596	GM12878	blood:	n/a	n/a
9	SIN3A	chr12:58228285-58228600	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:58228216..58229792-chr12:58282546..58284939,2	K562	blood:
2	chr12:58145252..58148251-chr12:58228552..58230766,2	MCF-7	breast:
3	chr12:58228537..58230716-chr12:58295563..58297383,2	MCF-7	breast:
4	chr12:58227798..58230136-chr12:58279373..58282138,2	MCF-7	breast:
5	chr12:58219255..58221070-chr12:58228307..58230908,2	K562	blood:
6	chr12:58228517..58230592-chr12:58298078..58299845,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000257953	TF binding region
ENSG00000135446	Chromatin interaction
ENSG00000175215	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 15 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10444569	0.81[AMR][1000 genomes]
rs10747784	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10747786	0.92[JPT][hapmap];0.80[AMR][1000 genomes]
rs10747787	0.92[JPT][hapmap];0.80[AMR][1000 genomes]
rs10783850	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10783851	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10783853	0.92[JPT][hapmap]
rs10783854	0.86[CEU][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10783855	0.86[CEU][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10783856	0.82[CEU][hapmap];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10877013	0.86[YRI][hapmap]
rs10877014	0.86[YRI][hapmap]
rs10877022	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10877024	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10877025	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10877026	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10877028	0.86[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap]
rs10877029	0.92[JPT][hapmap];0.85[AMR][1000 genomes]
rs10877030	0.92[JPT][hapmap];0.85[AMR][1000 genomes]
rs10877031	0.81[AMR][1000 genomes]
rs10877032	0.80[AMR][1000 genomes]
rs11172361	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11172362	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11172367	0.92[JPT][hapmap];0.80[AMR][1000 genomes]
rs11172369	0.86[JPT][hapmap]
rs12426201	0.81[AMR][1000 genomes]
rs1599750	0.86[CEU][hapmap];0.87[CHB][hapmap];0.85[JPT][hapmap];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1599751	0.86[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1599931	0.92[JPT][hapmap]
rs1875125	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4237844	0.92[JPT][hapmap];0.81[AMR][1000 genomes]
rs4646536	0.81[YRI][hapmap]
rs4760171	1.00[CEU][hapmap];0.83[CHB][hapmap];0.81[YRI][hapmap];0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4760172	0.92[JPT][hapmap];0.85[AMR][1000 genomes]
rs4760332	1.00[CEU][hapmap];0.83[CHB][hapmap];0.85[JPT][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4760333	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4760335	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4760339	0.85[JPT][hapmap];0.81[AMR][1000 genomes]
rs4760341	0.85[JPT][hapmap]
rs59401446	0.81[AMR][1000 genomes]
rs6581155	0.82[YRI][hapmap]
rs7312623	0.92[JPT][hapmap];0.81[AMR][1000 genomes]
rs870392	1.00[CEU][hapmap];0.83[CHB][hapmap];0.85[JPT][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs871871	1.00[CEU][hapmap];0.83[CHB][hapmap];0.85[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9645819	0.80[AMR][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
rs7489290	XRCC6BP1	cis	Artery Tibial	GTEx
rs7489290	FAM119B	cis	Cerebellum	GTEx
rs7489290	METTL21B	cis	Whole Blood	GTEx
rs7489290	XRCC6BP1	cis	Muscle Skeletal	GTEx
rs7489290	METTL21B	cis	Muscle Skeletal	GTEx
rs7489290	TSFM	Cis_1M	lymphoblastoid	RTeQTL
rs7489290	XRCC6BP1	cis	Heart Left Ventricle	GTEx
rs7489290	XRCC6BP1	cis	Skin Sun Exposed Lower leg	GTEx
rs7489290	FAM119B	Cis_1M	lymphoblastoid	RTeQTL
rs7489290	XRCC6BP1	Cis_1M	lymphoblastoid	RTeQTL
rs7489290	XRCC6BP1	cis	Whole Blood	GTEx
rs7489290	METTL21B	cis	Esophagus Muscularis	GTEx
rs7489290	FAM119B	cis	Frontal Cortex	GTEx
rs7489290	FAM119B	cis	Temporal Cortex	GTEx
rs7489290	XRCC6BP1	cis	lung	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:58222800-58230200	Enhancers	Right Atrium	heart
2	chr12:58222800-58230400	Genic enhancers	Fetal Stomach	stomach
3	chr12:58223000-58230400	Genic enhancers	Fetal Muscle Leg	muscle
4	chr12:58223400-58230400	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr12:58223400-58231000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr12:58223400-58236400	Enhancers	Right Ventricle	heart
7	chr12:58223600-58230400	Weak transcription	Hela-S3	cervix
8	chr12:58223600-58231600	Enhancers	Placenta	Placenta
9	chr12:58223800-58230800	Enhancers	Liver	Liver
10	chr12:58224000-58230200	Weak transcription	Dnd41	blood
11	chr12:58224200-58230600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr12:58224200-58238200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
13	chr12:58224400-58238000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr12:58224400-58238200	Enhancers	Spleen	Spleen
15	chr12:58224800-58229600	Enhancers	Primary B cells from peripheral blood	blood
16	chr12:58225000-58230200	Enhancers	Fetal Heart	heart
17	chr12:58225200-58237000	Enhancers	Cortex derived primary cultured neurospheres	brain
18	chr12:58225400-58235600	Genic enhancers	Fetal Intestine Small	intestine
19	chr12:58225600-58228600	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
20	chr12:58225600-58228600	Genic enhancers	Fetal Lung	lung
21	chr12:58225600-58229800	Enhancers	Primary neutrophils fromperipheralblood	blood
22	chr12:58225600-58232800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr12:58225600-58238200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
24	chr12:58225800-58229200	Enhancers	Breast Myoepithelial Primary Cells	Breast
25	chr12:58225800-58229200	Enhancers	Primary T cells from cord blood	blood
26	chr12:58225800-58229200	Enhancers	Brain Inferior Temporal Lobe	brain
27	chr12:58225800-58229400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr12:58225800-58229400	Enhancers	Primary T helper naive cells from peripheral blood	blood
29	chr12:58225800-58229400	Enhancers	Primary T helper cells PMA-I stimulated	--
30	chr12:58225800-58229400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr12:58225800-58229400	Enhancers	Monocytes-CD14+_RO01746	blood
32	chr12:58225800-58229600	Enhancers	Primary hematopoietic stem cells	blood
33	chr12:58225800-58229600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
34	chr12:58225800-58229800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
35	chr12:58225800-58229800	Enhancers	Rectal Mucosa Donor 29	rectum
36	chr12:58225800-58230000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
37	chr12:58225800-58230400	Weak transcription	A549	lung
38	chr12:58225800-58230600	Enhancers	Thymus	Thymus
39	chr12:58225800-58236000	Enhancers	Brain Angular Gyrus	brain
40	chr12:58226000-58229200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr12:58226000-58229200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr12:58226000-58229200	Enhancers	Adipose Nuclei	Adipose
43	chr12:58226000-58229200	Enhancers	NHLF	lung
44	chr12:58226000-58229400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr12:58226000-58229400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
46	chr12:58226000-58229400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
47	chr12:58226000-58229400	Enhancers	Colonic Mucosa	Colon
48	chr12:58226000-58229400	Enhancers	Duodenum Smooth Muscle	Duodenum
49	chr12:58226000-58229400	Weak transcription	HMEC	breast
50	chr12:58226000-58229400	Weak transcription	NHEK	skin

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