Variant report

Variant	rs17394420
Chromosome Location	chr15:49420816-49420817
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 54 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10519221	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1055254	0.93[MEX][hapmap];0.83[TSI][hapmap]
rs11630318	0.93[CEU][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11632038	0.86[CEU][hapmap];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11632211	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11632303	1.00[CEU][hapmap];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11634636	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11635005	0.93[CEU][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11635455	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11635814	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11638515	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs11638981	1.00[ASW][hapmap]
rs12913966	1.00[AFR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17394970	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17396119	1.00[CEU][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17396536	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17396612	0.82[CEU][hapmap];0.93[MEX][hapmap];0.83[TSI][hapmap]
rs17396747	1.00[CEU][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17397211	1.00[CEU][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17473148	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17473568	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17476361	0.93[CEU][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3088333	1.00[CEU][hapmap];1.00[GIH][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35692325	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4775800	0.88[EUR][1000 genomes]
rs57252806	1.00[ASN][1000 genomes]
rs57749497	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57785991	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61442055	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7162633	1.00[ASN][1000 genomes]
rs7165168	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7167474	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7177624	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73390343	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73390360	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73390362	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73390384	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73390392	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73392236	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73392249	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73392256	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73392277	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73392288	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73394324	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73394331	0.82[EUR][1000 genomes]
rs73394333	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73394339	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73394355	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73394359	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73396235	1.00[ASN][1000 genomes]
rs73396238	1.00[ASN][1000 genomes]
rs73408143	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8025550	0.82[CEU][hapmap];0.87[MEX][hapmap];0.83[TSI][hapmap]
rs8029506	0.81[CEU][hapmap]

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs17394420	SECISBP2L	cis	cerebellum	SCAN
rs17394420	TMEM62	cis	cerebellum	SCAN
rs17394420	MFAP1	cis	cerebellum	SCAN
rs17394420	SECISBP2L	cis	parietal	SCAN
rs17394420	TRPM7	cis	cerebellum	SCAN
rs17394420	LCMT2	cis	parietal	SCAN
rs17394420	FGF7	cis	Muscle Skeletal	GTEx

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:49388800-49434800	Weak transcription	Small Intestine	intestine
2	chr15:49395600-49426400	Weak transcription	Rectal Smooth Muscle	rectum
3	chr15:49398600-49427600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr15:49403000-49434600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr15:49403200-49423400	Weak transcription	Psoas Muscle	Psoas
6	chr15:49403400-49440200	Weak transcription	Pancreas	Pancrea
7	chr15:49403600-49423600	Weak transcription	Esophagus	oesophagus
8	chr15:49403600-49432200	Weak transcription	Fetal Stomach	stomach
9	chr15:49403600-49435200	Weak transcription	Aorta	Aorta
10	chr15:49403600-49435200	Weak transcription	Gastric	stomach
11	chr15:49403600-49435400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr15:49403800-49433200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr15:49404600-49424000	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr15:49404800-49423400	Weak transcription	HepG2	liver
15	chr15:49404800-49425600	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr15:49404800-49434600	Weak transcription	Right Ventricle	heart
17	chr15:49404800-49435000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr15:49405600-49441800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr15:49411400-49432200	Weak transcription	Fetal Intestine Small	intestine
20	chr15:49413000-49427200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr15:49413400-49426200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr15:49413600-49447000	Weak transcription	Stomach Mucosa	stomach
23	chr15:49413800-49421200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr15:49414000-49426400	Strong transcription	HSMM	muscle
25	chr15:49414800-49421200	Weak transcription	Colon Smooth Muscle	Colon
26	chr15:49415200-49423600	Weak transcription	Pancreatic Islets	Pancreatic Islet
27	chr15:49415200-49433400	Weak transcription	Lung	lung
28	chr15:49415400-49427400	Strong transcription	Hela-S3	cervix
29	chr15:49415400-49427600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr15:49415600-49427400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
31	chr15:49415600-49437600	Strong transcription	Primary monocytes fromperipheralblood	blood
32	chr15:49415800-49421200	Weak transcription	HSMMtube	muscle
33	chr15:49415800-49437400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr15:49416200-49427600	Weak transcription	Fetal Brain Male	brain
35	chr15:49416200-49437400	Strong transcription	Monocytes-CD14+_RO01746	blood
36	chr15:49416400-49427800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr15:49416800-49423600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr15:49416800-49436800	Strong transcription	Liver	Liver
39	chr15:49416800-49437200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr15:49417000-49437200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr15:49417200-49424400	Strong transcription	Duodenum Smooth Muscle	Duodenum
42	chr15:49417200-49424800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr15:49417200-49426600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr15:49417200-49436600	Strong transcription	Primary T helper cells PMA-I stimulated	--
45	chr15:49417200-49437200	Strong transcription	HUES48 Cell Line	embryonic stem cell
46	chr15:49417200-49437200	Strong transcription	HUES64 Cell Line	embryonic stem cell
47	chr15:49417200-49437400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
48	chr15:49417200-49437400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr15:49417400-49427600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
50	chr15:49417400-49427600	Strong transcription	Placenta	Placenta

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