Variant report

Variant	rs12914979
Chromosome Location	chr15:52677424-52677425
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:52676956..52678562-chr15:52682249..52684331,2	MCF-7	breast:

Extended variants
information (count: 53 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs1001522	0.88[CEU][hapmap];0.84[CHB][hapmap];0.93[JPT][hapmap]
rs10083671	0.88[CEU][hapmap];0.86[JPT][hapmap]
rs10083673	0.88[CEU][hapmap];0.91[CHB][hapmap];0.93[JPT][hapmap];0.90[YRI][hapmap];0.83[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs1009157	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10467925	0.96[CEU][hapmap];0.82[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10518687	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1125460	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12324100	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12324121	1.00[CEU][hapmap];0.81[CHB][hapmap];0.89[YRI][hapmap];0.86[EUR][1000 genomes]
rs12909874	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs1464963	0.88[CEU][hapmap];0.91[CHB][hapmap];0.93[JPT][hapmap];0.90[YRI][hapmap];0.80[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs1464964	0.82[ASN][1000 genomes]
rs1669856	0.82[ASN][1000 genomes]
rs1669858	0.88[CEU][hapmap];0.92[CHB][hapmap];0.93[JPT][hapmap];0.82[ASN][1000 genomes]
rs1669867	0.89[CEU][hapmap];0.91[CHB][hapmap];0.93[JPT][hapmap]
rs1724628	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1724629	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1724631	0.82[ASN][1000 genomes]
rs1724634	0.82[ASN][1000 genomes]
rs1724641	0.85[CEU][hapmap];0.84[CHB][hapmap];0.93[JPT][hapmap]
rs17542017	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2242057	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2242058	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2414150	1.00[CEU][hapmap];0.91[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2414151	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs2444013	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35134548	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3858907	0.93[CEU][hapmap];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4280181	1.00[CEU][hapmap];0.83[CHB][hapmap];0.81[JPT][hapmap];0.90[YRI][hapmap];0.86[EUR][1000 genomes]
rs4519295	0.96[CEU][hapmap];0.91[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4606660	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4776037	0.91[CEU][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4776039	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4776046	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs62015999	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62023267	0.84[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs71474804	0.83[ASN][1000 genomes]
rs7176061	0.84[CHB][hapmap];0.93[JPT][hapmap]
rs7176482	1.00[CEU][hapmap];0.90[CHB][hapmap];0.93[JPT][hapmap];0.89[YRI][hapmap];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7176639	1.00[CEU][hapmap];0.91[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7182150	1.00[CEU][hapmap];0.92[CHB][hapmap];0.93[JPT][hapmap];0.91[YRI][hapmap];0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs722436	0.80[AMR][1000 genomes]
rs752864	0.81[CHB][hapmap];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs752865	1.00[CEU][hapmap];0.81[CHB][hapmap];0.92[EUR][1000 genomes]
rs752866	1.00[CEU][hapmap];0.81[CHB][hapmap];0.93[EUR][1000 genomes]
rs8028033	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8033626	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8038386	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs935892	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1846455	chr15:52501831-52714452	Strong transcription Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
2	nsv471245	chr15:52607262-53187165	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
3	nsv1041421	chr15:52661342-53148286	Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
4	nsv1054899	chr15:52662365-52803756	Enhancers Genic enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12914979	ARPP-19	Cis_1M	lymphoblastoid	RTeQTL
rs12914979	MYO5A	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:52609800-52677600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr15:52630600-52684800	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr15:52631600-52679200	Weak transcription	Fetal Intestine Small	intestine
4	chr15:52644200-52680800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr15:52644600-52730200	Weak transcription	Esophagus	oesophagus
6	chr15:52647400-52690600	Strong transcription	Primary neutrophils fromperipheralblood	blood
7	chr15:52649000-52687200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
8	chr15:52649600-52677600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
9	chr15:52658400-52687200	Weak transcription	Small Intestine	intestine
10	chr15:52662600-52683600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr15:52662600-52685000	Weak transcription	Psoas Muscle	Psoas
12	chr15:52663200-52711400	Strong transcription	Monocytes-CD14+_RO01746	blood
13	chr15:52663400-52708600	Strong transcription	Primary monocytes fromperipheralblood	blood
14	chr15:52665200-52720600	Weak transcription	Pancreas	Pancrea
15	chr15:52667000-52679600	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr15:52667000-52682000	Weak transcription	Rectal Mucosa Donor 31	rectum
17	chr15:52667000-52684800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr15:52667000-52686000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr15:52667000-52686600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr15:52667600-52684400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr15:52668000-52683400	Weak transcription	H1 Cell Line	embryonic stem cell
22	chr15:52668800-52679400	Weak transcription	NH-A	brain
23	chr15:52668800-52683800	Weak transcription	HUES64 Cell Line	embryonic stem cell
24	chr15:52668800-52730400	Weak transcription	Aorta	Aorta
25	chr15:52669200-52683400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
26	chr15:52669400-52693400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
27	chr15:52671200-52682000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr15:52671400-52681400	Strong transcription	Primary T helper cells fromperipheralblood	blood
29	chr15:52672000-52679600	Weak transcription	Duodenum Mucosa	Duodenum
30	chr15:52672400-52684000	Weak transcription	Fetal Heart	heart
31	chr15:52673800-52683800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
32	chr15:52673800-52684800	Weak transcription	Hela-S3	cervix
33	chr15:52673800-52730200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
34	chr15:52674000-52677600	Weak transcription	Placenta	Placenta
35	chr15:52674000-52678000	Weak transcription	HSMMtube	muscle
36	chr15:52674000-52703800	Weak transcription	Fetal Brain Male	brain
37	chr15:52674800-52681400	Strong transcription	Primary B cells from peripheral blood	blood
38	chr15:52675000-52686200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr15:52675000-52697400	Weak transcription	Fetal Muscle Trunk	muscle
40	chr15:52675200-52677600	Genic enhancers	HUVEC	blood vessel
41	chr15:52676000-52677800	Strong transcription	Brain Anterior Caudate	brain
42	chr15:52676000-52679600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
43	chr15:52676000-52683200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
44	chr15:52676000-52684600	Weak transcription	Osteobl	bone
45	chr15:52676000-52705600	Weak transcription	Fetal Stomach	stomach
46	chr15:52676200-52677800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
47	chr15:52676200-52679800	Weak transcription	Primary T helper cells PMA-I stimulated	--
48	chr15:52676200-52683400	Weak transcription	HUES48 Cell Line	embryonic stem cell
49	chr15:52676200-52686400	Weak transcription	Fetal Muscle Leg	muscle
50	chr15:52676200-52696800	Weak transcription	Rectal Mucosa Donor 29	rectum

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