Variant report

Variant	rs6493346
Chromosome Location	chr15:49314476-49314477
allele	G/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	POLR2A	chr15:49314257-49314479	K562	blood:	n/a	n/a

Variant related genes	Relation type
SECISBP2L	TF binding region

Extended variants
information (count: 29 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs1054307	0.96[CEU][hapmap];0.85[GIH][hapmap];0.88[JPT][hapmap];0.96[MEX][hapmap];0.84[MKK][hapmap];0.93[TSI][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10775139	0.81[CEU][hapmap]
rs11070682	0.88[CEU][hapmap];0.82[TSI][hapmap]
rs11638215	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11855740	1.00[CEU][hapmap];0.88[JPT][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11858917	0.82[ASN][1000 genomes]
rs12903559	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12904344	0.85[CHB][hapmap]
rs12909616	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16962017	0.93[ASW][hapmap];0.89[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.88[ASN][1000 genomes]
rs2899427	0.88[CEU][hapmap];0.82[TSI][hapmap]
rs4284578	1.00[CEU][hapmap];0.88[JPT][hapmap];0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4423366	0.83[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs4536401	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4774536	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4775790	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4775792	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4775795	1.00[CEU][hapmap];0.88[JPT][hapmap];0.90[YRI][hapmap];0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4775796	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7164309	0.88[YRI][hapmap]
rs7165264	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7166261	0.82[ASN][1000 genomes]
rs7167402	1.00[CEU][hapmap];0.85[GIH][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.95[TSI][hapmap];0.85[YRI][hapmap];0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7359317	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs8029751	0.95[CHB][hapmap]
rs8029914	1.00[CEU][hapmap];0.83[GIH][hapmap];0.82[JPT][hapmap];0.96[MEX][hapmap];0.83[MKK][hapmap];0.93[TSI][hapmap];0.90[YRI][hapmap];0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs8037958	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs877007	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9920913	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6493346	SECISBP2L	cis	cerebellum	SCAN
rs6493346	GALK2	cis	Whole Blood	GTEx
rs6493346	GALK2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:49282800-49333400	Weak transcription	A549	lung
2	chr15:49283600-49337600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr15:49285000-49329000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr15:49289200-49336400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr15:49289800-49317000	Weak transcription	Stomach Mucosa	stomach
6	chr15:49298000-49328400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr15:49298000-49328800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr15:49298200-49314600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr15:49298200-49314600	Strong transcription	Adipose Nuclei	Adipose
10	chr15:49298200-49316200	Strong transcription	Rectal Mucosa Donor 29	rectum
11	chr15:49298200-49316400	Strong transcription	Placenta	Placenta
12	chr15:49298200-49329800	Strong transcription	Primary T helper cells fromperipheralblood	blood
13	chr15:49298400-49322000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr15:49298400-49322000	Strong transcription	Primary B cells from peripheral blood	blood
15	chr15:49298600-49325200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr15:49298600-49329600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr15:49301400-49329000	Weak transcription	K562	blood
18	chr15:49303000-49327600	Weak transcription	Right Ventricle	heart
19	chr15:49304200-49318800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr15:49304400-49318000	Weak transcription	Brain Germinal Matrix	brain
21	chr15:49308400-49318200	Weak transcription	Fetal Brain Female	brain
22	chr15:49308400-49320000	Weak transcription	HepG2	liver
23	chr15:49308400-49320200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
24	chr15:49308400-49327000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr15:49308400-49327600	Weak transcription	Dnd41	blood
26	chr15:49308600-49318000	Weak transcription	Brain Angular Gyrus	brain
27	chr15:49308600-49319000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr15:49308600-49320000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr15:49308600-49320600	Weak transcription	Fetal Heart	heart
30	chr15:49308600-49323000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr15:49308600-49326800	Weak transcription	Esophagus	oesophagus
32	chr15:49308600-49327000	Weak transcription	Gastric	stomach
33	chr15:49308800-49315600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
34	chr15:49308800-49320000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
35	chr15:49308800-49326800	Weak transcription	Fetal Thymus	thymus
36	chr15:49308800-49328200	Weak transcription	Small Intestine	intestine
37	chr15:49308800-49331800	Weak transcription	H9 Cell Line	embryonic stem cell
38	chr15:49308800-49334400	Weak transcription	Psoas Muscle	Psoas
39	chr15:49309200-49327600	Weak transcription	NHEK	skin
40	chr15:49309400-49317000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
41	chr15:49309400-49318000	Weak transcription	Primary hematopoietic stem cells	blood
42	chr15:49309400-49318200	Weak transcription	Fetal Brain Male	brain
43	chr15:49309400-49320000	Weak transcription	Colonic Mucosa	Colon
44	chr15:49309600-49315400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
45	chr15:49309600-49318000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
46	chr15:49309600-49318000	Weak transcription	Rectal Mucosa Donor 31	rectum
47	chr15:49309600-49319000	Weak transcription	H1 Cell Line	embryonic stem cell
48	chr15:49309600-49320200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
49	chr15:49309600-49321600	Weak transcription	HMEC	breast
50	chr15:49309800-49317600	Weak transcription	iPS-18 Cell Line	embryonic stem cell

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