Variant report

Variant	rs12909519
Chromosome Location	chr15:51341867-51341868
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:51336449..51337958-chr15:51340592..51342315,2	K562	blood:
2	chr15:51333377..51335540-chr15:51340391..51342855,2	K562	blood:
3	chr15:51339931..51341975-chr15:51352347..51354430,2	MCF-7	breast:
4	chr15:51333522..51338506-chr15:51338654..51346011,6	MCF-7	breast:

Extended variants
information (count: 99 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:89)

rs_ID	r²[population]
rs10744956	0.82[CHB][hapmap]
rs11070824	0.82[CHB][hapmap];0.82[JPT][hapmap]
rs11070829	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11070835	0.91[CHB][hapmap]
rs1147129	0.84[CHD][hapmap];0.82[JPT][hapmap]
rs1147131	0.82[JPT][hapmap]
rs11632971	0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11635015	0.96[CEU][hapmap];0.86[CHB][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11635102	0.96[CEU][hapmap];0.86[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11857810	0.81[CHB][hapmap]
rs12438343	0.82[JPT][hapmap];0.80[ASN][1000 genomes]
rs12441714	0.89[AFR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12595034	0.80[ASN][1000 genomes]
rs12708425	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1276854	0.82[JPT][hapmap];1.00[YRI][hapmap]
rs12898208	0.80[ASN][1000 genomes]
rs12898530	0.80[ASN][1000 genomes]
rs12904382	1.00[CEU][hapmap];0.91[CHB][hapmap];0.86[JPT][hapmap];0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12906866	0.81[JPT][hapmap];0.85[YRI][hapmap];0.84[ASN][1000 genomes]
rs12912295	0.86[EUR][1000 genomes]
rs1371058	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1472946	0.82[CHB][hapmap]
rs1509423	0.95[CEU][hapmap];0.83[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1550336	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1550340	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17703090	0.82[CHB][hapmap]
rs2118785	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2127367	0.80[ASN][1000 genomes]
rs2127368	0.82[JPT][hapmap];0.80[ASN][1000 genomes]
rs2170011	0.80[ASN][1000 genomes]
rs2249535	0.84[CHD][hapmap];0.82[JPT][hapmap];0.86[YRI][hapmap]
rs2306331	0.83[CHD][hapmap];0.82[JPT][hapmap]
rs2306332	0.88[AFR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2414081	0.82[JPT][hapmap];0.80[ASN][1000 genomes]
rs2614776	0.82[JPT][hapmap]
rs2614779	0.82[JPT][hapmap]
rs2614780	0.84[CHD][hapmap];0.82[JPT][hapmap]
rs2614781	0.82[JPT][hapmap];0.86[YRI][hapmap]
rs2614790	0.82[JPT][hapmap];0.84[YRI][hapmap]
rs2614791	0.82[CHB][hapmap]
rs2614794	0.82[JPT][hapmap];0.86[YRI][hapmap]
rs2619686	0.82[JPT][hapmap];0.86[YRI][hapmap]
rs2663533	0.85[CHD][hapmap];0.81[JPT][hapmap]
rs2663535	0.81[JPT][hapmap]
rs2663538	0.82[JPT][hapmap]
rs2663553	0.82[JPT][hapmap]
rs2663554	0.81[JPT][hapmap]
rs2663556	0.82[JPT][hapmap];0.86[YRI][hapmap]
rs3743045	1.00[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3784302	0.87[CEU][hapmap];0.81[GIH][hapmap]
rs3784303	0.82[JPT][hapmap]
rs4438254	0.80[ASN][1000 genomes]
rs4444282	0.88[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs4775910	0.82[CHB][hapmap]
rs4775913	0.85[ASN][1000 genomes]
rs56115630	0.88[ASN][1000 genomes]
rs6493469	0.84[CHD][hapmap];0.82[JPT][hapmap]
rs6493471	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6493472	0.83[ASN][1000 genomes]
rs6493473	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6493476	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs67145268	0.84[ASN][1000 genomes]
rs67228714	0.87[ASN][1000 genomes]
rs714784	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7162209	1.00[ASW][hapmap];0.96[CEU][hapmap];0.86[CHB][hapmap];0.91[CHD][hapmap];0.95[GIH][hapmap];0.82[JPT][hapmap];0.97[LWK][hapmap];0.91[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7168385	0.82[JPT][hapmap];0.80[ASN][1000 genomes]
rs7168846	0.82[JPT][hapmap];0.80[ASN][1000 genomes]
rs7169888	0.80[ASN][1000 genomes]
rs7170311	0.81[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs7170365	0.80[ASN][1000 genomes]
rs7170675	0.84[CHD][hapmap];0.82[JPT][hapmap];0.80[ASN][1000 genomes]
rs7171085	0.80[ASN][1000 genomes]
rs7177267	0.80[ASN][1000 genomes]
rs7180258	0.81[CHB][hapmap];0.82[JPT][hapmap];0.83[ASN][1000 genomes]
rs7181051	0.80[ASN][1000 genomes]
rs7181201	0.81[CHB][hapmap];0.86[CHD][hapmap];0.86[JPT][hapmap];0.88[ASN][1000 genomes]
rs7182957	0.82[JPT][hapmap];0.84[ASN][1000 genomes]
rs7184026	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73408568	0.82[ASN][1000 genomes]
rs8024428	0.80[ASN][1000 genomes]
rs8025456	0.88[ASN][1000 genomes]
rs8026318	1.00[CEU][hapmap];0.81[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8029155	0.84[CHD][hapmap];0.82[JPT][hapmap]
rs8029369	0.82[JPT][hapmap];0.80[ASN][1000 genomes]
rs8030124	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8030214	0.96[CEU][hapmap];0.86[CHB][hapmap];0.82[JPT][hapmap];0.91[MEX][hapmap];0.90[MKK][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs8031702	0.84[CHD][hapmap];0.82[JPT][hapmap];0.86[YRI][hapmap]
rs8033934	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8035358	0.95[CEU][hapmap];0.86[CHB][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1047443	chr15:50744781-51647023	Strong transcription Active TSS Weak transcription Genic enhancers Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
2	nsv569399	chr15:50874964-51562198	Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
3	nsv569400	chr15:50874964-51767265	ZNF genes & repeats Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
4	nsv1038778	chr15:51196641-51356728	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
5	nsv904214	chr15:51204364-51535192	Strong transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
6	nsv1049644	chr15:51265447-51560445	Strong transcription Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
7	esv34532	chr15:51276128-51752856	Flanking Active TSS Weak transcription Strong transcription Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
8	esv2758382	chr15:51282257-51830339	Enhancers Bivalent/Poised TSS Weak transcription Bivalent Enhancer Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
9	esv2760031	chr15:51282257-51830339	Weak transcription Enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
10	nsv428634	chr15:51299632-51446666	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12909519	GABPB1	cis	parietal	SCAN

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:51332000-51347000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr15:51336400-51346800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr15:51336600-51344000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr15:51339400-51342000	Enhancers	Right Atrium	heart
5	chr15:51339600-51343800	Weak transcription	Psoas Muscle	Psoas
6	chr15:51339600-51344000	Weak transcription	Fetal Muscle Trunk	muscle
7	chr15:51339600-51345000	Weak transcription	HSMM	muscle
8	chr15:51339800-51343600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr15:51339800-51343600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
10	chr15:51339800-51343800	Weak transcription	Rectal Smooth Muscle	rectum
11	chr15:51339800-51344000	Weak transcription	Brain Germinal Matrix	brain
12	chr15:51339800-51344000	Weak transcription	HSMMtube	muscle
13	chr15:51339800-51344400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr15:51339800-51345800	Weak transcription	Muscle Satellite Cultured Cells	--
15	chr15:51339800-51346800	Weak transcription	Aorta	Aorta
16	chr15:51339800-51348000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr15:51340000-51342000	Enhancers	Primary monocytes fromperipheralblood	blood
18	chr15:51340000-51343800	Weak transcription	Duodenum Smooth Muscle	Duodenum
19	chr15:51340000-51344400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr15:51340000-51347800	Weak transcription	HUVEC	blood vessel
21	chr15:51340200-51342000	Enhancers	Monocytes-CD14+_RO01746	blood
22	chr15:51340200-51343600	Weak transcription	Adipose Nuclei	Adipose
23	chr15:51340200-51343600	Weak transcription	Brain Hippocampus Middle	brain
24	chr15:51340200-51346800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
25	chr15:51340200-51352800	Weak transcription	Brain Anterior Caudate	brain
26	chr15:51340400-51342000	Enhancers	Primary B cells from peripheral blood	blood
27	chr15:51340400-51342400	Enhancers	GM12878-XiMat	blood
28	chr15:51340400-51343600	Weak transcription	Colon Smooth Muscle	Colon
29	chr15:51340400-51349600	Weak transcription	Rectal Mucosa Donor 29	rectum
30	chr15:51340600-51343600	Weak transcription	Fetal Muscle Leg	muscle
31	chr15:51340600-51343600	Weak transcription	Skeletal Muscle Female	skeletal muscle
32	chr15:51340600-51343800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr15:51340600-51343800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr15:51340600-51343800	Weak transcription	Brain Substantia Nigra	brain
35	chr15:51340600-51343800	Weak transcription	Spleen	Spleen
36	chr15:51340600-51344200	Weak transcription	Lung	lung
37	chr15:51340600-51344200	Weak transcription	Stomach Smooth Muscle	stomach
38	chr15:51340600-51344400	Weak transcription	Colonic Mucosa	Colon
39	chr15:51340600-51346800	Weak transcription	HUES6 Cell Line	embryonic stem cell
40	chr15:51340600-51348800	Weak transcription	Stomach Mucosa	stomach
41	chr15:51340800-51342000	Enhancers	iPS-20b Cell Line	embryonic stem cell
42	chr15:51340800-51343800	Weak transcription	Sigmoid Colon	Sigmoid Colon
43	chr15:51340800-51344200	Weak transcription	Left Ventricle	heart
44	chr15:51340800-51344200	Weak transcription	Ovary	ovary
45	chr15:51340800-51351800	Weak transcription	Fetal Intestine Small	intestine
46	chr15:51341000-51342000	Enhancers	Cortex derived primary cultured neurospheres	brain
47	chr15:51341000-51343800	Weak transcription	Small Intestine	intestine
48	chr15:51341200-51342000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr15:51341200-51342000	Enhancers	Pancreas	Pancrea
50	chr15:51341400-51343800	Weak transcription	Fetal Lung	lung

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