Variant report

Variant	rs17396612
Chromosome Location	chr15:49549943-49549944
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 129 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:118)

rs_ID	r²[population]
rs10519211	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs10519221	0.80[EUR][1000 genomes]
rs10519229	1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap]
rs1055254	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1114003	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs11630318	1.00[MEX][hapmap];0.83[TSI][hapmap];0.81[EUR][1000 genomes]
rs11632303	0.82[CEU][hapmap]
rs11634636	0.81[EUR][1000 genomes]
rs11635005	1.00[MEX][hapmap];0.83[TSI][hapmap];0.81[EUR][1000 genomes]
rs11635308	0.88[MEX][hapmap];0.80[TSI][hapmap]
rs11635354	0.80[CEU][hapmap]
rs11635455	0.81[CEU][hapmap]
rs11638515	0.82[CEU][hapmap]
rs16962065	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs16962067	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs16962101	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs16962112	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs16962139	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs16962146	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs16962147	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs16962163	0.82[ASN][1000 genomes]
rs16962166	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs16962169	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs16962171	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs16962174	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs16962175	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs16962177	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs16962187	1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[ASN][1000 genomes]
rs16962189	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs16962196	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs16962202	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs16962205	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs16962209	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs16962211	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs16962213	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs16962235	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs16962236	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs16962237	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs16962238	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs16962244	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs16962256	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs16962257	1.00[CHB][hapmap];0.88[CHD][hapmap]
rs16962259	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs16962262	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs16962273	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs16962274	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs16962276	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs16962288	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs16962296	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs16962307	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs16962308	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs16962314	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs16962327	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs16962331	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs16962416	1.00[CHB][hapmap]
rs17394420	0.82[CEU][hapmap];0.93[MEX][hapmap];0.83[TSI][hapmap]
rs17394970	0.82[CEU][hapmap]
rs17396119	0.82[CEU][hapmap];0.81[EUR][1000 genomes]
rs17396536	0.82[CEU][hapmap];0.82[EUR][1000 genomes]
rs17396747	0.82[CEU][hapmap];0.81[EUR][1000 genomes]
rs17397211	0.81[CEU][hapmap];0.81[EUR][1000 genomes]
rs17400706	0.94[MEX][hapmap]
rs17426226	0.82[ASN][1000 genomes]
rs17473148	0.82[CEU][hapmap]
rs17473568	0.82[CEU][hapmap];0.81[MEX][hapmap];0.83[TSI][hapmap]
rs17475228	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17476361	0.81[EUR][1000 genomes]
rs17476940	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17477722	1.00[MEX][hapmap];0.86[TSI][hapmap]
rs17478618	0.94[MEX][hapmap]
rs2059935	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2078024	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2127243	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2169931	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2279192	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2289391	0.82[ASN][1000 genomes]
rs2899437	1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap]
rs3088333	0.82[CEU][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap]
rs35692325	0.81[EUR][1000 genomes]
rs3784630	0.81[AFR][1000 genomes];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3959659	0.88[ASN][1000 genomes]
rs57560518	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs57749497	0.81[EUR][1000 genomes]
rs59356430	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6493354	0.88[ASN][1000 genomes]
rs7165168	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7167474	0.81[EUR][1000 genomes]
rs7167852	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7168633	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7173759	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs7176949	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs7179094	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs7179907	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs7181656	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs7182449	0.82[ASN][1000 genomes]
rs7183899	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs73392233	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73392236	0.82[AMR][1000 genomes]
rs73392249	0.82[AMR][1000 genomes]
rs73392262	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73392277	0.81[EUR][1000 genomes]
rs73392288	0.81[EUR][1000 genomes]
rs73394324	0.81[EUR][1000 genomes]
rs73394331	0.81[EUR][1000 genomes]
rs73394333	0.81[EUR][1000 genomes]
rs73394339	0.81[EUR][1000 genomes]
rs73394355	0.81[EUR][1000 genomes]
rs73394357	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73394359	0.82[EUR][1000 genomes]
rs73396206	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8025550	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8028746	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs8029506	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8031680	1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap]
rs8033311	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8035829	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs8035901	0.88[ASN][1000 genomes]
rs8039469	0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1039220	chr15:49492509-49644261	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv569342	chr15:49529302-49549943	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
3	nsv569347	chr15:49534702-49549943	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv569354	chr15:49540216-49549943	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
5	nsv569364	chr15:49545009-49549943	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
6	nsv569365	chr15:49545009-49557933	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
7	nsv569374	chr15:49545192-49549943	Active TSS Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
8	nsv569375	chr15:49545192-49557933	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
9	nsv569385	chr15:49545780-49549943	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
10	nsv569390	chr15:49546263-49549943	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
11	nsv569391	chr15:49546424-49549943	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs17396612	TRPM7	cis	cerebellum	SCAN
rs17396612	LCMT2	cis	parietal	SCAN
rs17396612	SECISBP2L	cis	parietal	SCAN
rs17396612	DUOXA2	cis	cerebellum	SCAN
rs17396612	FGF7	cis	Muscle Skeletal	GTEx
rs17396612	MFAP1	cis	cerebellum	SCAN
rs17396612	C15orf33	cis	cerebellum	SCAN

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:49518600-49557600	Weak transcription	Esophagus	oesophagus
2	chr15:49520400-49595600	Weak transcription	Right Ventricle	heart
3	chr15:49522400-49559400	Weak transcription	Pancreas	Pancrea
4	chr15:49528000-49576000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr15:49529200-49550600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr15:49533800-49576200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
7	chr15:49535600-49557000	Weak transcription	Fetal Intestine Small	intestine
8	chr15:49535600-49564600	Weak transcription	Rectal Mucosa Donor 29	rectum
9	chr15:49535600-49574200	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr15:49535600-49574200	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr15:49535800-49563400	Weak transcription	NH-A	brain
12	chr15:49535800-49566800	Weak transcription	Left Ventricle	heart
13	chr15:49535800-49575800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr15:49536200-49553200	Weak transcription	Primary B cells from cord blood	blood
15	chr15:49537600-49566000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr15:49538600-49550400	Weak transcription	HSMM	muscle
17	chr15:49539400-49553200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr15:49539600-49563000	Weak transcription	Ovary	ovary
19	chr15:49540000-49550400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
20	chr15:49540000-49550400	Weak transcription	NHDF-Ad	bronchial
21	chr15:49540000-49552200	Weak transcription	Fetal Muscle Leg	muscle
22	chr15:49540000-49566200	Weak transcription	K562	blood
23	chr15:49540000-49577600	Weak transcription	Small Intestine	intestine
24	chr15:49540200-49552200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
25	chr15:49540600-49557400	Weak transcription	Cortex derived primary cultured neurospheres	brain
26	chr15:49541400-49551400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr15:49541400-49562600	Weak transcription	Dnd41	blood
28	chr15:49541600-49557200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
29	chr15:49541600-49575000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
30	chr15:49541600-49595800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr15:49541800-49558800	Weak transcription	Primary T cells fromperipheralblood	blood
32	chr15:49542000-49560800	Weak transcription	Monocytes-CD14+_RO01746	blood
33	chr15:49542200-49557200	Weak transcription	Primary hematopoietic stem cells	blood
34	chr15:49542400-49550600	Weak transcription	Primary T helper cells PMA-I stimulated	--
35	chr15:49542800-49560800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr15:49543000-49550600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr15:49543200-49550200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr15:49543200-49558000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr15:49543800-49564600	Weak transcription	Duodenum Mucosa	Duodenum
40	chr15:49543800-49574200	Weak transcription	Primary T helper cells fromperipheralblood	blood
41	chr15:49546000-49550800	Weak transcription	Primary monocytes fromperipheralblood	blood
42	chr15:49546400-49550400	Weak transcription	Primary T cells from cord blood	blood
43	chr15:49546400-49557200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
44	chr15:49548400-49550400	Weak transcription	Osteobl	bone
45	chr15:49548400-49562200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr15:49548600-49550400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr15:49548600-49553200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr15:49548800-49575800	Weak transcription	Stomach Smooth Muscle	stomach
49	chr15:49549400-49550400	Weak transcription	Pancreatic Islets	Pancreatic Islet
50	chr15:49549400-49575200	Weak transcription	Hela-S3	cervix

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