Variant report

Variant	rs17473568
Chromosome Location	chr15:49441523-49441524
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:49440196..49442233-chr15:49445854..49447948,2	MCF-7	breast:
2	chr15:49439437..49443597-chr15:49460944..49463407,4	MCF-7	breast:
3	chr15:49438116..49443617-chr15:49443933..49448726,7	K562	blood:
4	chr15:49411597..49414274-chr15:49439381..49441889,2	K562	blood:
5	chr15:49409539..49411389-chr15:49441274..49443184,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000166200	Chromatin interaction
ENSG00000259467	Chromatin interaction
ENSG00000156958	Chromatin interaction
ENSG00000264210	Chromatin interaction

Extended variants
information (count: 64 )
Associated
traits (count: 7 )

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

rs_ID	r²[population]
rs10519221	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1055254	0.81[MEX][hapmap];0.83[TSI][hapmap]
rs11630318	1.00[ASW][hapmap];0.93[CEU][hapmap];0.95[LWK][hapmap];0.81[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11632038	0.86[CEU][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11632211	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11632303	1.00[CEU][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11632575	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11633282	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11634636	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11635005	0.93[CEU][hapmap];0.95[LWK][hapmap];0.81[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11635455	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11635814	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11638515	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs11638606	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12913966	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17394420	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]
rs17394970	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17396119	1.00[CEU][hapmap];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17396536	1.00[CEU][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17396612	0.82[CEU][hapmap];0.81[MEX][hapmap];0.83[TSI][hapmap]
rs17396747	1.00[CEU][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17397211	1.00[CEU][hapmap];1.00[YRI][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17473148	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17476361	0.93[CEU][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17476940	0.81[MEX][hapmap];0.83[TSI][hapmap]
rs2078024	0.81[MEX][hapmap];0.83[TSI][hapmap]
rs3088333	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.95[LWK][hapmap];0.81[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35692325	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4775800	0.85[EUR][1000 genomes]
rs57252806	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57560518	0.80[EUR][1000 genomes]
rs57749497	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57785991	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59112977	1.00[ASN][1000 genomes]
rs60594237	1.00[ASN][1000 genomes]
rs61442055	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7162633	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7165168	0.84[AFR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7167474	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7177624	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73390343	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73390360	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73390362	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73390384	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73390392	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73392233	0.80[EUR][1000 genomes]
rs73392236	0.89[AFR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73392249	0.89[AFR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73392256	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73392277	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73392288	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73394324	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73394331	0.84[EUR][1000 genomes]
rs73394333	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73394339	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73394355	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73394359	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73396235	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73396238	1.00[ASN][1000 genomes]
rs73398223	1.00[ASN][1000 genomes]
rs73408143	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8025550	0.82[CEU][hapmap];0.83[TSI][hapmap];0.80[EUR][1000 genomes]
rs8027094	1.00[ASN][1000 genomes]
rs8029506	0.81[CEU][hapmap]

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs17473568	SECISBP2L	cis	cerebellum	SCAN
rs17473568	SECISBP2L	cis	parietal	SCAN
rs17473568	TRPM7	cis	cerebellum	SCAN
rs17473568	TMEM62	cis	cerebellum	SCAN
rs17473568	LCMT2	cis	parietal	SCAN
rs17473568	MFAP1	cis	cerebellum	SCAN
rs17473568	FGF7	cis	Muscle Skeletal	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:49405600-49441800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr15:49413600-49447000	Weak transcription	Stomach Mucosa	stomach
3	chr15:49419000-49445800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr15:49420200-49447000	Weak transcription	Spleen	Spleen
5	chr15:49420400-49447000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr15:49429200-49447000	Weak transcription	Esophagus	oesophagus
7	chr15:49433800-49446600	Weak transcription	Fetal Intestine Small	intestine
8	chr15:49435200-49445800	Weak transcription	Fetal Heart	heart
9	chr15:49435600-49446600	Weak transcription	Right Ventricle	heart
10	chr15:49435800-49442800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr15:49435800-49442800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr15:49435800-49443000	Weak transcription	Colonic Mucosa	Colon
13	chr15:49435800-49443000	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr15:49435800-49445400	Weak transcription	Brain Germinal Matrix	brain
15	chr15:49435800-49445600	Weak transcription	Fetal Brain Male	brain
16	chr15:49435800-49445600	Weak transcription	Rectal Mucosa Donor 29	rectum
17	chr15:49435800-49446000	Weak transcription	Fetal Kidney	kidney
18	chr15:49435800-49446000	Weak transcription	Stomach Smooth Muscle	stomach
19	chr15:49435800-49446600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr15:49435800-49446600	Weak transcription	HSMMtube	muscle
21	chr15:49435800-49446800	Weak transcription	Aorta	Aorta
22	chr15:49435800-49446800	Weak transcription	Fetal Muscle Trunk	muscle
23	chr15:49436000-49444800	Weak transcription	Lung	lung
24	chr15:49436000-49445200	Weak transcription	Thymus	Thymus
25	chr15:49436000-49446000	Weak transcription	Rectal Mucosa Donor 31	rectum
26	chr15:49436000-49446600	Weak transcription	Fetal Stomach	stomach
27	chr15:49436000-49446600	Weak transcription	Fetal Thymus	thymus
28	chr15:49436000-49446800	Weak transcription	H9 Cell Line	embryonic stem cell
29	chr15:49436000-49446800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr15:49436000-49447000	Weak transcription	Gastric	stomach
31	chr15:49436000-49447000	Weak transcription	Sigmoid Colon	Sigmoid Colon
32	chr15:49436200-49446600	Weak transcription	Fetal Lung	lung
33	chr15:49436200-49446600	Weak transcription	Fetal Muscle Leg	muscle
34	chr15:49436200-49447000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr15:49436400-49441600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr15:49436400-49447000	Weak transcription	Left Ventricle	heart
37	chr15:49437000-49441600	Weak transcription	HUES6 Cell Line	embryonic stem cell
38	chr15:49437000-49444600	Weak transcription	Dnd41	blood
39	chr15:49437000-49446600	Weak transcription	Fetal Brain Female	brain
40	chr15:49437200-49445200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr15:49437200-49445800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr15:49437200-49445800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr15:49437200-49445800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
44	chr15:49437200-49446000	Weak transcription	H1 Cell Line	embryonic stem cell
45	chr15:49437200-49446000	Weak transcription	Fetal Intestine Large	intestine
46	chr15:49437200-49446800	Weak transcription	Primary T cells fromperipheralblood	blood
47	chr15:49437400-49441800	Enhancers	Primary T helper cells fromperipheralblood	blood
48	chr15:49437400-49445000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr15:49437400-49446000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr15:49437400-49446800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood

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