Variant report

Variant	rs2899430
Chromosome Location	chr15:49514285-49514286
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:49509199..49512109-chr15:49514145..49516432,2	MCF-7	breast:

Extended variants
information (count: 96 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:95)

rs_ID	r²[population]
rs10467992	1.00[CEU][hapmap];0.85[CHB][hapmap];0.95[YRI][hapmap];0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1048975	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs10775139	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs10851475	0.88[CEU][hapmap]
rs11070682	1.00[CHB][hapmap]
rs11070692	0.92[CEU][hapmap]
rs11629547	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11632063	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11633810	0.84[CHB][hapmap];0.89[JPT][hapmap]
rs11858114	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12438777	0.85[CHB][hapmap];0.89[JPT][hapmap]
rs12902875	0.81[ASN][1000 genomes]
rs12904344	0.85[CHB][hapmap];0.80[JPT][hapmap]
rs1429556	0.92[CEU][hapmap]
rs1812926	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1864299	0.84[CHB][hapmap];0.83[JPT][hapmap]
rs1981995	0.84[CHB][hapmap];0.89[JPT][hapmap]
rs2086256	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2127241	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2127242	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2127244	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2169932	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2219812	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];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2247517	0.85[CHB][hapmap];0.89[JPT][hapmap]
rs2263559	0.98[ASN][1000 genomes]
rs2413935	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2413937	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2413939	0.81[AMR][1000 genomes]
rs2457228	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2580923	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2580926	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2663088	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2663089	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs2663090	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28437582	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28479967	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28539950	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28728368	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28731311	0.96[ASN][1000 genomes]
rs2899427	1.00[CHB][hapmap];0.94[JPT][hapmap]
rs2899431	0.85[CHB][hapmap];0.89[JPT][hapmap]
rs2919148	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2940745	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2940746	0.98[ASN][1000 genomes]
rs3098613	0.84[CHB][hapmap];0.89[JPT][hapmap]
rs3098615	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3098619	0.84[CHB][hapmap];0.89[JPT][hapmap]
rs3098620	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3098621	0.85[CHB][hapmap];0.89[JPT][hapmap]
rs3105858	0.85[CHB][hapmap];0.89[JPT][hapmap]
rs3105861	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3105863	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3105864	0.84[CHB][hapmap];0.89[JPT][hapmap]
rs3105866	0.85[CHB][hapmap];0.89[JPT][hapmap]
rs34854443	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3907313	0.85[CHB][hapmap];0.89[JPT][hapmap]
rs4774537	0.85[CHB][hapmap];0.89[JPT][hapmap]
rs4775804	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4775805	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4775807	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs481466	0.84[CHB][hapmap];0.89[JPT][hapmap]
rs489813	0.89[CHB][hapmap]
rs490621	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs500122	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55736202	0.96[ASN][1000 genomes]
rs563533	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs568726	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs600863	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs603868	0.92[ASN][1000 genomes]
rs604765	0.85[CHB][hapmap];0.89[JPT][hapmap]
rs612803	0.85[CHB][hapmap];0.89[JPT][hapmap]
rs626295	0.84[CHB][hapmap];0.89[JPT][hapmap]
rs626855	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs647118	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap]
rs6493356	0.85[CHB][hapmap];0.88[JPT][hapmap]
rs6493357	0.90[CHB][hapmap];0.87[JPT][hapmap]
rs6493361	0.96[CEU][hapmap];0.80[CHB][hapmap];0.95[YRI][hapmap];0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6493363	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[YRI][hapmap];0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs671945	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs679957	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs685172	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs7166847	0.85[CHB][hapmap];0.89[JPT][hapmap]
rs7167338	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7167555	0.85[YRI][hapmap];0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7176455	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7179127	0.84[CHB][hapmap];0.83[JPT][hapmap]
rs735495	0.88[CEU][hapmap]
rs754165	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs754166	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8025952	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8034661	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs8034747	0.92[CEU][hapmap]
rs8039512	0.85[CHB][hapmap];0.94[JPT][hapmap]
rs8040075	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9806748	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2899430	GALK2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:81 , 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	chr15:49492800-49514600	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr15:49493000-49520000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
13	chr15:49494000-49518600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
14	chr15:49495000-49515600	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr15:49495000-49515800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
16	chr15:49495000-49518000	Weak transcription	Placenta	Placenta
17	chr15:49495200-49520200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr15:49503600-49524000	Weak transcription	HepG2	liver
19	chr15:49504200-49520200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr15:49504200-49530800	Weak transcription	Fetal Thymus	thymus
21	chr15:49507200-49517400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr15:49507400-49515600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr15:49508600-49515600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr15:49508600-49517400	Weak transcription	Right Ventricle	heart
25	chr15:49508800-49515000	Weak transcription	Fetal Muscle Trunk	muscle
26	chr15:49508800-49515800	Weak transcription	Psoas Muscle	Psoas
27	chr15:49508800-49517400	Weak transcription	Esophagus	oesophagus
28	chr15:49508800-49517600	Weak transcription	Spleen	Spleen
29	chr15:49508800-49521600	Weak transcription	Hela-S3	cervix
30	chr15:49508800-49535800	Weak transcription	A549	lung
31	chr15:49509000-49517400	Weak transcription	Primary T cells fromperipheralblood	blood
32	chr15:49509000-49517400	Weak transcription	Pancreas	Pancrea
33	chr15:49509000-49517400	Weak transcription	Right Atrium	heart
34	chr15:49509200-49517400	Weak transcription	Primary B cells from cord blood	blood
35	chr15:49509200-49517400	Weak transcription	Gastric	stomach
36	chr15:49509200-49517800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr15:49509400-49517200	Weak transcription	Fetal Heart	heart
38	chr15:49509400-49527400	Weak transcription	Brain Cingulate Gyrus	brain
39	chr15:49510000-49541800	Weak transcription	NHEK	skin
40	chr15:49510200-49524600	Weak transcription	Primary neutrophils fromperipheralblood	blood
41	chr15:49510200-49537000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
42	chr15:49510800-49534400	Weak transcription	Muscle Satellite Cultured Cells	--
43	chr15:49511000-49515200	Weak transcription	K562	blood
44	chr15:49511000-49527600	Weak transcription	Dnd41	blood
45	chr15:49511200-49516600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr15:49511200-49517400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr15:49511200-49517600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr15:49511200-49517600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
49	chr15:49511200-49519800	Weak transcription	Primary B cells from peripheral blood	blood
50	chr15:49511200-49527400	Weak transcription	Osteobl	bone

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