Variant report

Variant	rs58644322
Chromosome Location	chr6:109684287-109684288
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:109682199..109685973-chr6:109687053..109690833,5	MCF-7	breast:
2	chr6:109658622..109660807-chr6:109682756..109684452,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000203799	Chromatin interaction

Extended variants
information (count: 63 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs1046943	0.86[EUR][1000 genomes]
rs1074765	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1074766	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10872033	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11251	0.95[EUR][1000 genomes]
rs12214147	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12529733	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13219952	0.93[EUR][1000 genomes]
rs1476387	0.93[EUR][1000 genomes]
rs1521907	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17070591	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1853330	0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1885690	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1885691	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2211288	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2236084	0.86[EUR][1000 genomes]
rs2277113	0.88[EUR][1000 genomes]
rs2884037	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35146243	0.86[EUR][1000 genomes]
rs3734652	0.86[EUR][1000 genomes]
rs3757230	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3757231	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3757235	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3778474	0.95[EUR][1000 genomes]
rs3778478	0.86[EUR][1000 genomes]
rs3818933	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4636056	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4945831	0.93[EUR][1000 genomes]
rs4946967	0.95[EUR][1000 genomes]
rs4946970	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4946976	0.88[EUR][1000 genomes]
rs59597139	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6914216	0.92[EUR][1000 genomes]
rs6920372	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6939548	0.86[EUR][1000 genomes]
rs6939953	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs699700	0.95[EUR][1000 genomes]
rs730089	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs736830	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs746794	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7748669	0.90[EUR][1000 genomes]
rs7751582	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7754650	0.92[EUR][1000 genomes]
rs7768973	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8465	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs910730	0.89[EUR][1000 genomes]
rs9320286	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9372213	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9386799	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9480947	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9480949	0.91[EUR][1000 genomes]
rs9480956	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9480958	0.93[EUR][1000 genomes]
rs9487064	0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9487066	0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9487069	0.95[EUR][1000 genomes]
rs9487070	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9487076	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9487084	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9487085	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9487103	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs974034	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9791241	0.86[EUR][1000 genomes]

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs58644322	SMPD2	cis	Esophagus Mucosa	GTEx
rs58644322	RP11-425D10.10	cis	Skin Sun Exposed Lower leg	GTEx
rs58644322	ZBTB24	Cis_1M	lymphoblastoid	RTeQTL
rs58644322	RP11-425D10.10	cis	Whole Blood	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:109673600-109687000	Weak transcription	Right Ventricle	heart
2	chr6:109675000-109684600	Strong transcription	Stomach Smooth Muscle	stomach
3	chr6:109675000-109691800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr6:109675000-109692600	Strong transcription	Primary neutrophils fromperipheralblood	blood
5	chr6:109675000-109693200	Strong transcription	Monocytes-CD14+_RO01746	blood
6	chr6:109675000-109694400	Strong transcription	Rectal Mucosa Donor 29	rectum
7	chr6:109675000-109694600	Strong transcription	Primary T cells fromperipheralblood	blood
8	chr6:109675000-109700800	Strong transcription	Placenta	Placenta
9	chr6:109675200-109684400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr6:109675200-109688800	Strong transcription	Primary T cells from cord blood	blood
11	chr6:109675200-109693200	Strong transcription	Duodenum Smooth Muscle	Duodenum
12	chr6:109675400-109691400	Strong transcription	Osteobl	bone
13	chr6:109676800-109693800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
14	chr6:109677000-109687200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
15	chr6:109677000-109698200	Strong transcription	Fetal Intestine Large	intestine
16	chr6:109677600-109695000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
17	chr6:109677800-109700600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr6:109678200-109687800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr6:109678200-109691400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr6:109678200-109694600	Strong transcription	Fetal Thymus	thymus
21	chr6:109678200-109695200	Strong transcription	Duodenum Mucosa	Duodenum
22	chr6:109678400-109685400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
23	chr6:109678400-109694400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
24	chr6:109678400-109694400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr6:109678600-109693200	Strong transcription	Primary T helper cells PMA-I stimulated	--
26	chr6:109678600-109693400	Strong transcription	Primary T helper cells fromperipheralblood	blood
27	chr6:109678800-109684600	Strong transcription	Sigmoid Colon	Sigmoid Colon
28	chr6:109678800-109695400	Strong transcription	Rectal Mucosa Donor 31	rectum
29	chr6:109678800-109699000	Strong transcription	Dnd41	blood
30	chr6:109679000-109688200	Strong transcription	Cortex derived primary cultured neurospheres	brain
31	chr6:109679000-109693200	Strong transcription	K562	blood
32	chr6:109679200-109700400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr6:109679400-109689000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
34	chr6:109679400-109700600	Strong transcription	HUES6 Cell Line	embryonic stem cell
35	chr6:109680400-109697200	Weak transcription	Fetal Brain Male	brain
36	chr6:109680600-109700600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr6:109680800-109688200	Weak transcription	Colon Smooth Muscle	Colon
38	chr6:109680800-109694400	Strong transcription	Primary B cells from peripheral blood	blood
39	chr6:109681000-109689400	Weak transcription	Brain Angular Gyrus	brain
40	chr6:109681400-109686400	Strong transcription	Brain Anterior Caudate	brain
41	chr6:109681600-109685800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr6:109682400-109692600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr6:109682600-109686000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
44	chr6:109682600-109700800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
45	chr6:109683000-109684400	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr6:109683000-109685000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr6:109683000-109685600	Strong transcription	Fetal Stomach	stomach
48	chr6:109683200-109684400	Strong transcription	H1 Cell Line	embryonic stem cell
49	chr6:109683200-109684600	Strong transcription	Hela-S3	cervix
50	chr6:109683200-109699800	Strong transcription	iPS-18 Cell Line	embryonic stem cell

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