Variant report

Variant	rs8039899
Chromosome Location	chr15:57288378-57288379
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	chr15:57286745..57288660-chr15:57302090..57304157,2	MCF-7	breast:

Extended variants
information (count: 91 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:85)

rs_ID	r²[population]
rs10467927	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[YRI][hapmap]
rs10467928	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs10467929	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs10851612	0.86[CHB][hapmap];0.86[JPT][hapmap]
rs11071303	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11071308	0.82[CHB][hapmap];0.90[JPT][hapmap]
rs1115019	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs11856210	0.86[CHB][hapmap];0.90[JPT][hapmap]
rs11856411	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12901355	0.84[EUR][1000 genomes]
rs13379847	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap]
rs1430820	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1430822	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1441236	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs1657922	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs16977153	0.86[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs16977222	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs16977243	1.00[CEU][hapmap];0.95[CHB][hapmap]
rs16977270	0.86[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs16977278	0.82[CHB][hapmap];0.90[JPT][hapmap]
rs17415731	0.86[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs1820994	0.86[ASN][1000 genomes]
rs2169467	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs2278613	0.87[CHB][hapmap];0.86[JPT][hapmap]
rs2464429	0.96[YRI][hapmap]
rs2464430	0.96[YRI][hapmap]
rs2470079	0.93[YRI][hapmap]
rs2470082	0.96[YRI][hapmap]
rs2593211	0.81[CHB][hapmap];0.90[JPT][hapmap]
rs2593249	0.82[CHB][hapmap];0.90[JPT][hapmap]
rs2593252	0.93[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs2703576	0.93[YRI][hapmap]
rs2703614	0.85[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs2733188	0.93[YRI][hapmap]
rs2733333	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs2733334	0.82[CHB][hapmap];0.90[JPT][hapmap]
rs28360967	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28422021	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs28505122	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs28533433	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28541606	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs28612876	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28616268	0.85[EUR][1000 genomes]
rs28648577	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28649108	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28654848	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28677775	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28756149	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28814080	0.85[AFR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28856894	0.88[EUR][1000 genomes]
rs2920267	0.96[YRI][hapmap]
rs2951899	0.92[YRI][hapmap]
rs2951903	0.93[YRI][hapmap]
rs2951904	0.92[YRI][hapmap]
rs2962991	0.96[YRI][hapmap]
rs2962992	0.92[YRI][hapmap]
rs4774245	0.86[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs6493900	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs6493902	0.92[YRI][hapmap]
rs7162194	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7163267	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap]
rs7164655	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[YRI][hapmap];0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7169053	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7171073	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7171304	1.00[CEU][hapmap];0.90[YRI][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7173748	0.95[CHB][hapmap];0.91[JPT][hapmap]
rs7175191	0.86[CHB][hapmap];0.86[JPT][hapmap]
rs7175436	0.85[YRI][hapmap]
rs7176873	0.92[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7178833	1.00[CHB][hapmap];0.95[JPT][hapmap];0.88[YRI][hapmap];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8023343	0.86[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap]
rs8023816	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8026702	0.82[CHB][hapmap];0.90[JPT][hapmap]
rs8031516	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8031640	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8032615	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8033010	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8034066	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8034502	0.82[CHB][hapmap];0.91[JPT][hapmap]
rs8035485	0.86[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs8035916	0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs8040708	0.94[EUR][1000 genomes]
rs9302200	1.00[CEU][hapmap];0.82[CHB][hapmap];0.85[JPT][hapmap];0.87[EUR][1000 genomes]
rs9806170	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.96[YRI][hapmap]
rs9806199	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1042486	chr15:57094598-57505992	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
2	nsv542393	chr15:57115116-57341363	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
3	nsv904250	chr15:57225766-57294085	ZNF genes & repeats Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
4	nsv1052052	chr15:57232111-57344561	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
5	nsv542394	chr15:57232111-57344561	Enhancers Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
6	nsv904251	chr15:57241970-57575916	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs8039899	LOC283663	Cis_1M	lymphoblastoid	RTeQTL
rs8039899	TCF12	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:76 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:57269800-57304800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr15:57273000-57307200	Weak transcription	Fetal Intestine Small	intestine
3	chr15:57274200-57289200	Weak transcription	Fetal Muscle Leg	muscle
4	chr15:57274200-57295600	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr15:57275400-57306200	Weak transcription	Duodenum Mucosa	Duodenum
6	chr15:57276200-57289200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
7	chr15:57276200-57313400	Weak transcription	Primary T cells fromperipheralblood	blood
8	chr15:57276800-57288600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr15:57277000-57313400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr15:57278600-57295400	Weak transcription	NH-A	brain
11	chr15:57279400-57300000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr15:57279600-57301800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
13	chr15:57279800-57300200	Weak transcription	Psoas Muscle	Psoas
14	chr15:57280600-57294000	Weak transcription	HSMMtube	muscle
15	chr15:57282000-57289200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
16	chr15:57282000-57289800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
17	chr15:57282000-57295400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr15:57282000-57295400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr15:57282000-57295600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr15:57282000-57307400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr15:57282000-57315000	Weak transcription	Primary T helper cells fromperipheralblood	blood
22	chr15:57282200-57288400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr15:57282200-57288400	Weak transcription	HMEC	breast
24	chr15:57282200-57288400	Weak transcription	NHDF-Ad	bronchial
25	chr15:57282200-57288400	Weak transcription	Osteobl	bone
26	chr15:57282200-57291800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr15:57282200-57295000	Weak transcription	HUES48 Cell Line	embryonic stem cell
28	chr15:57282200-57295200	Weak transcription	Hela-S3	cervix
29	chr15:57282200-57295200	Weak transcription	NHLF	lung
30	chr15:57282200-57295600	Weak transcription	Duodenum Smooth Muscle	Duodenum
31	chr15:57282200-57295800	Weak transcription	Fetal Kidney	kidney
32	chr15:57282200-57298600	Weak transcription	Ovary	ovary
33	chr15:57282200-57299400	Weak transcription	Primary T helper cells PMA-I stimulated	--
34	chr15:57282200-57308400	Weak transcription	Thymus	Thymus
35	chr15:57282200-57311000	Weak transcription	K562	blood
36	chr15:57282200-57315200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
37	chr15:57282400-57288600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr15:57282600-57288400	Weak transcription	Brain Anterior Caudate	brain
39	chr15:57282600-57289800	Strong transcription	Fetal Thymus	thymus
40	chr15:57282600-57293800	Weak transcription	Fetal Heart	heart
41	chr15:57282600-57306200	Weak transcription	HepG2	liver
42	chr15:57283400-57291800	Weak transcription	Left Ventricle	heart
43	chr15:57283400-57291800	Weak transcription	Right Atrium	heart
44	chr15:57283800-57296400	Weak transcription	Fetal Stomach	stomach
45	chr15:57284200-57310800	Weak transcription	Fetal Muscle Trunk	muscle
46	chr15:57285800-57289000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr15:57286000-57289200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
48	chr15:57286000-57290400	Weak transcription	Cortex derived primary cultured neurospheres	brain
49	chr15:57286000-57295200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr15:57286000-57295400	Weak transcription	HUES64 Cell Line	embryonic stem cell

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