Variant report

Variant	rs59056467
Chromosome Location	chr6:109767931-109767932
allele	A/C/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:109766673..109769201-chr6:109798430..109801986,3	MCF-7	breast:
2	chr6:109739441..109742103-chr6:109765700..109768387,2	MCF-7	breast:
3	chr6:109767345..109770309-chr6:109802803..109805406,2	MCF-7	breast:
4	chr6:109701746..109704787-chr6:109765536..109768393,4	K562	blood:
5	chr6:109756751..109759661-chr6:109767137..109769430,2	MCF-7	breast:
6	chr6:109701777..109705568-chr6:109765713..109769272,5	K562	blood:
7	chr6:109701880..109704518-chr6:109765827..109768290,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000112365	Chromatin interaction
ENSG00000135535	Chromatin interaction
ENSG00000260273	Chromatin interaction

Extended variants
information (count: 64 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs10080429	0.82[EUR][1000 genomes]
rs1040284	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10457190	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1048203	0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10782161	0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10782162	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10872034	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11153174	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11153175	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11153176	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11153177	0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11153180	0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11153181	0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11967108	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12190920	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12190996	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12192847	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12193493	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12197114	0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12206928	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12209691	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12213313	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12524273	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12524639	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12528822	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs13212766	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1322816	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1358997	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1358998	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1546980	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1590306	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs17070580	0.83[EUR][1000 genomes]
rs1923725	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2236582	0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2275650	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs34202013	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35056702	0.83[EUR][1000 genomes]
rs36035949	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs36099706	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3757234	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3778475	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3778477	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3799839	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3807005	0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3818934	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs59906308	0.96[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs68042406	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6916579	0.80[AMR][1000 genomes]
rs6929023	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7372	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs752262	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7773095	0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9320287	0.83[EUR][1000 genomes]
rs9480948	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9480951	0.83[EUR][1000 genomes]
rs9480953	0.83[EUR][1000 genomes]
rs9480955	0.83[EUR][1000 genomes]
rs9480957	0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9487068	0.81[EUR][1000 genomes]
rs9487094	0.83[EUR][1000 genomes]
rs9487095	0.83[EUR][1000 genomes]
rs9487098	0.81[EUR][1000 genomes]
rs9487100	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9885646	0.83[EUR][1000 genomes]

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs59056467	SMPD2	cis	Whole Blood	GTEx
rs59056467	RP11-425D10.10	cis	Esophagus Mucosa	GTEx
rs59056467	RP11-425D10.10	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:109762800-109775800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr6:109763200-109774400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr6:109763200-109775600	Weak transcription	Fetal Kidney	kidney
4	chr6:109763200-109775800	Weak transcription	HUVEC	blood vessel
5	chr6:109763400-109768600	Strong transcription	iPS-15b Cell Line	embryonic stem cell
6	chr6:109763400-109770400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr6:109763400-109775000	Strong transcription	NHLF	lung
8	chr6:109763400-109775200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr6:109763600-109768200	Strong transcription	Fetal Lung	lung
10	chr6:109763600-109768400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr6:109763600-109768400	Strong transcription	HUES6 Cell Line	embryonic stem cell
12	chr6:109763600-109768400	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr6:109763600-109768400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr6:109763600-109768600	Strong transcription	HUES48 Cell Line	embryonic stem cell
15	chr6:109763600-109768600	Strong transcription	HUES64 Cell Line	embryonic stem cell
16	chr6:109763600-109768800	Strong transcription	H1 Cell Line	embryonic stem cell
17	chr6:109763600-109768800	Strong transcription	Brain Anterior Caudate	brain
18	chr6:109763600-109769400	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr6:109763600-109769600	Weak transcription	Brain Substantia Nigra	brain
20	chr6:109763600-109770000	Strong transcription	NHEK	skin
21	chr6:109763600-109770800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
22	chr6:109763600-109773200	Weak transcription	Fetal Brain Male	brain
23	chr6:109763600-109775000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr6:109763600-109775200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr6:109763600-109775800	Weak transcription	Right Atrium	heart
26	chr6:109763800-109768000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
27	chr6:109763800-109768000	Strong transcription	Brain Hippocampus Middle	brain
28	chr6:109763800-109768400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr6:109763800-109768400	Strong transcription	Liver	Liver
30	chr6:109763800-109769000	Strong transcription	Primary neutrophils fromperipheralblood	blood
31	chr6:109763800-109769000	Strong transcription	Monocytes-CD14+_RO01746	blood
32	chr6:109763800-109769600	Strong transcription	Fetal Muscle Leg	muscle
33	chr6:109763800-109769800	Strong transcription	Thymus	Thymus
34	chr6:109763800-109770600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
35	chr6:109763800-109770600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr6:109763800-109770800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
37	chr6:109763800-109771000	Strong transcription	Fetal Intestine Small	intestine
38	chr6:109763800-109774400	Strong transcription	HSMM	muscle
39	chr6:109763800-109774600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr6:109763800-109774800	Strong transcription	Fetal Stomach	stomach
41	chr6:109763800-109774800	Weak transcription	Small Intestine	intestine
42	chr6:109763800-109775400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
43	chr6:109763800-109775400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr6:109763800-109775600	Weak transcription	HepG2	liver
45	chr6:109764000-109768400	Strong transcription	Primary T helper cells PMA-I stimulated	--
46	chr6:109764000-109768400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
47	chr6:109764000-109768600	Strong transcription	Duodenum Mucosa	Duodenum
48	chr6:109764000-109768800	Strong transcription	Primary B cells from cord blood	blood
49	chr6:109764000-109768800	Strong transcription	Primary T cells from cord blood	blood
50	chr6:109764000-109769200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell

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