Variant report

Variant	rs8025550
Chromosome Location	chr15:49515067-49515068
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:49447415..49449082-chr15:49514596..49516737,2	MCF-7	breast:
2	chr15:49509199..49512109-chr15:49514145..49516432,2	MCF-7	breast:
3	chr15:49446271..49448785-chr15:49514644..49517454,2	MCF-7	breast:

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

Extended variants
information (count: 113 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:112)

rs_ID	r²[population]
rs10519211	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs1055254	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.94[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1114003	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs11630318	0.94[MEX][hapmap];0.83[TSI][hapmap]
rs11632211	0.86[EUR][1000 genomes]
rs11632303	0.82[CEU][hapmap];0.82[EUR][1000 genomes]
rs11635005	0.94[MEX][hapmap];0.83[TSI][hapmap]
rs11635354	0.80[CEU][hapmap]
rs11635455	0.81[CEU][hapmap];0.80[EUR][1000 genomes]
rs11635814	0.82[EUR][1000 genomes]
rs11638515	0.82[CEU][hapmap];0.82[EUR][1000 genomes]
rs12913966	0.83[EUR][1000 genomes]
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];0.85[ASN][1000 genomes]
rs16962139	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs16962146	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs16962147	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs16962163	0.85[ASN][1000 genomes]
rs16962166	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs16962169	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs16962171	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs16962174	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs16962175	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs16962177	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs16962187	1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[ASN][1000 genomes]
rs16962189	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs16962196	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs16962202	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs16962205	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs16962209	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs16962211	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs16962213	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[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];0.87[MEX][hapmap];0.83[TSI][hapmap]
rs17394970	0.82[CEU][hapmap];0.80[EUR][1000 genomes]
rs17396119	0.82[CEU][hapmap];0.80[EUR][1000 genomes]
rs17396536	0.82[CEU][hapmap]
rs17396612	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]
rs17396747	0.82[CEU][hapmap]
rs17397211	0.81[CEU][hapmap]
rs17426226	0.85[ASN][1000 genomes]
rs17473148	0.82[CEU][hapmap]
rs17473568	0.82[CEU][hapmap];0.83[TSI][hapmap];0.80[EUR][1000 genomes]
rs17475228	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17476940	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17477722	0.94[MEX][hapmap];0.86[TSI][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];0.94[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[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	0.85[ASN][1000 genomes]
rs3088333	0.82[CEU][hapmap];0.94[MEX][hapmap];0.83[TSI][hapmap]
rs3784630	0.80[AMR][1000 genomes]
rs3959659	0.91[ASN][1000 genomes]
rs57560518	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57785991	0.82[EUR][1000 genomes]
rs59356430	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61442055	0.80[EUR][1000 genomes]
rs6493354	0.91[ASN][1000 genomes]
rs7165168	0.82[AMR][1000 genomes]
rs7167852	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7168633	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[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];0.85[ASN][1000 genomes]
rs7177624	0.82[EUR][1000 genomes]
rs7179094	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs7179907	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs7181656	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs7182449	0.85[ASN][1000 genomes]
rs7183899	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs73390343	0.81[EUR][1000 genomes]
rs73390360	0.81[EUR][1000 genomes]
rs73390362	0.81[EUR][1000 genomes]
rs73390384	0.81[EUR][1000 genomes]
rs73390392	0.82[EUR][1000 genomes]
rs73392233	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73392236	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs73392249	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs73392256	0.84[EUR][1000 genomes]
rs73392262	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73392277	0.80[EUR][1000 genomes]
rs73392288	0.80[EUR][1000 genomes]
rs73394357	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73396206	0.80[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8028746	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs8029506	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8033311	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8035829	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs8035901	0.91[ASN][1000 genomes]
rs8039469	0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 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

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs8025550	DUOXA2	cis	cerebellum	SCAN
rs8025550	SECISBP2L	cis	parietal	SCAN
rs8025550	MFAP1	cis	cerebellum	SCAN
rs8025550	FGF7	cis	Muscle Skeletal	GTEx
rs8025550	C15orf33	cis	cerebellum	SCAN
rs8025550	TRPM7	cis	cerebellum	SCAN
rs8025550	LCMT2	cis	parietal	SCAN
rs8025550	SPANXN3	trans	brain	seeQTL

Chromatin state (count:79 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:49463600-49517600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr15:49463600-49527800	Weak transcription	HSMM	muscle
3	chr15:49463600-49540200	Weak transcription	Colonic Mucosa	Colon
4	chr15:49484200-49519400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
5	chr15:49487200-49531200	Weak transcription	HMEC	breast
6	chr15:49492000-49517600	Weak transcription	NHLF	lung
7	chr15:49492000-49520000	Weak transcription	Skeletal Muscle Male	skeletal muscle
8	chr15:49492000-49527800	Weak transcription	Rectal Smooth Muscle	rectum
9	chr15:49492000-49530200	Weak transcription	Stomach Smooth Muscle	stomach
10	chr15:49492000-49539400	Weak transcription	Small Intestine	intestine
11	chr15:49493000-49520000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
12	chr15:49494000-49518600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
13	chr15:49495000-49515600	Weak transcription	Rectal Mucosa Donor 31	rectum
14	chr15:49495000-49515800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
15	chr15:49495000-49518000	Weak transcription	Placenta	Placenta
16	chr15:49495200-49520200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr15:49503600-49524000	Weak transcription	HepG2	liver
18	chr15:49504200-49520200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr15:49504200-49530800	Weak transcription	Fetal Thymus	thymus
20	chr15:49507200-49517400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr15:49507400-49515600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr15:49508600-49515600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr15:49508600-49517400	Weak transcription	Right Ventricle	heart
24	chr15:49508800-49515800	Weak transcription	Psoas Muscle	Psoas
25	chr15:49508800-49517400	Weak transcription	Esophagus	oesophagus
26	chr15:49508800-49517600	Weak transcription	Spleen	Spleen
27	chr15:49508800-49521600	Weak transcription	Hela-S3	cervix
28	chr15:49508800-49535800	Weak transcription	A549	lung
29	chr15:49509000-49517400	Weak transcription	Primary T cells fromperipheralblood	blood
30	chr15:49509000-49517400	Weak transcription	Pancreas	Pancrea
31	chr15:49509000-49517400	Weak transcription	Right Atrium	heart
32	chr15:49509200-49517400	Weak transcription	Primary B cells from cord blood	blood
33	chr15:49509200-49517400	Weak transcription	Gastric	stomach
34	chr15:49509200-49517800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr15:49509400-49517200	Weak transcription	Fetal Heart	heart
36	chr15:49509400-49527400	Weak transcription	Brain Cingulate Gyrus	brain
37	chr15:49510000-49541800	Weak transcription	NHEK	skin
38	chr15:49510200-49524600	Weak transcription	Primary neutrophils fromperipheralblood	blood
39	chr15:49510200-49537000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
40	chr15:49510800-49534400	Weak transcription	Muscle Satellite Cultured Cells	--
41	chr15:49511000-49515200	Weak transcription	K562	blood
42	chr15:49511000-49527600	Weak transcription	Dnd41	blood
43	chr15:49511200-49516600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr15:49511200-49517400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr15:49511200-49517600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr15:49511200-49517600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
47	chr15:49511200-49519800	Weak transcription	Primary B cells from peripheral blood	blood
48	chr15:49511200-49527400	Weak transcription	Osteobl	bone
49	chr15:49511400-49517400	Weak transcription	Aorta	Aorta
50	chr15:49511400-49517400	Weak transcription	Duodenum Mucosa	Duodenum

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