Variant report

Variant	rs6493476
Chromosome Location	chr15:51367231-51367232
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:51365899..51367526-chr15:51369188..51370738,2	MCF-7	breast:
2	chr15:51353785..51356534-chr15:51367189..51369023,2	K562	blood:
3	chr15:51200864..51202454-chr15:51366982..51369964,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000081014	Chromatin interaction

Extended variants
information (count: 132 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:121)

rs_ID	r²[population]
rs10744956	0.82[CHB][hapmap];0.85[CHD][hapmap];0.82[JPT][hapmap]
rs10851494	0.81[JPT][hapmap]
rs11070824	0.82[CHB][hapmap];0.95[JPT][hapmap]
rs11070829	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11070835	0.91[CHB][hapmap]
rs1147128	0.82[ASN][1000 genomes]
rs1147129	0.91[CHD][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs1147130	0.82[ASN][1000 genomes]
rs1147131	0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs1147133	0.82[ASN][1000 genomes]
rs1147135	0.82[ASN][1000 genomes]
rs1147136	0.82[ASN][1000 genomes]
rs1147139	0.81[ASN][1000 genomes]
rs11632971	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11635015	0.96[CEU][hapmap];0.86[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11635102	0.96[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11854175	0.81[ASN][1000 genomes]
rs11857810	0.81[CHB][hapmap]
rs12438343	0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs12441714	0.87[AFR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12595034	0.84[ASN][1000 genomes]
rs12708425	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12898208	0.84[ASN][1000 genomes]
rs12898530	0.84[ASN][1000 genomes]
rs12904125	0.81[ASN][1000 genomes]
rs12904382	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12905611	0.81[ASN][1000 genomes]
rs12906866	0.95[JPT][hapmap];0.85[YRI][hapmap];0.87[ASN][1000 genomes]
rs12909519	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12912295	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12916407	0.82[ASN][1000 genomes]
rs1371058	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1472946	0.82[CHB][hapmap];0.82[JPT][hapmap]
rs1509423	0.95[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1550336	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1550340	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17703090	0.82[CHB][hapmap];0.82[JPT][hapmap]
rs2118785	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2127366	0.82[ASN][1000 genomes]
rs2127367	0.84[ASN][1000 genomes]
rs2127368	0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs2170011	0.84[ASN][1000 genomes]
rs2249535	0.91[CHD][hapmap];0.95[JPT][hapmap];0.86[YRI][hapmap];0.82[ASN][1000 genomes]
rs2306331	0.91[CHD][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs2306332	0.85[AFR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2414078	0.82[ASN][1000 genomes]
rs2414079	0.82[ASN][1000 genomes]
rs2414081	0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs2614776	0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs2614779	0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs2614780	0.91[CHD][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs2614781	0.95[JPT][hapmap];0.86[YRI][hapmap];0.82[ASN][1000 genomes]
rs2614782	0.82[ASN][1000 genomes]
rs2614784	0.82[ASN][1000 genomes]
rs2614789	0.82[ASN][1000 genomes]
rs2614790	0.95[JPT][hapmap];0.84[YRI][hapmap];0.82[ASN][1000 genomes]
rs2614791	0.82[CHB][hapmap];0.82[JPT][hapmap]
rs2614792	0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs2614794	0.95[JPT][hapmap];0.86[YRI][hapmap];0.82[ASN][1000 genomes]
rs2619686	0.95[JPT][hapmap];0.86[YRI][hapmap];0.82[ASN][1000 genomes]
rs2619687	0.82[ASN][1000 genomes]
rs2619688	0.82[ASN][1000 genomes]
rs2619693	0.80[ASN][1000 genomes]
rs2619694	0.81[ASN][1000 genomes]
rs2663533	0.93[CHD][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs2663535	0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs2663537	0.82[ASN][1000 genomes]
rs2663538	0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs2663541	0.82[ASN][1000 genomes]
rs2663543	0.82[ASN][1000 genomes]
rs2663544	0.82[ASN][1000 genomes]
rs2663545	0.82[ASN][1000 genomes]
rs2663546	0.82[ASN][1000 genomes]
rs2663553	0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs2663554	0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs2663555	0.82[ASN][1000 genomes]
rs3743045	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3784301	0.84[CHD][hapmap];0.86[JPT][hapmap]
rs3784302	0.87[CEU][hapmap];0.86[CHD][hapmap];0.81[GIH][hapmap];0.86[JPT][hapmap];0.83[MEX][hapmap];0.81[ASN][1000 genomes]
rs3784303	0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs4438254	0.84[ASN][1000 genomes]
rs4444282	0.85[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs4534781	0.83[ASN][1000 genomes]
rs4775910	0.82[CHB][hapmap];0.82[JPT][hapmap]
rs4775913	0.88[ASN][1000 genomes]
rs55939501	0.81[ASN][1000 genomes]
rs56115630	0.90[ASN][1000 genomes]
rs6493469	0.91[CHD][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs6493471	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6493472	0.86[ASN][1000 genomes]
rs6493473	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs67145268	0.88[ASN][1000 genomes]
rs67228714	0.89[ASN][1000 genomes]
rs714784	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7162209	1.00[ASW][hapmap];0.96[CEU][hapmap];0.86[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.97[LWK][hapmap];0.96[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7168385	0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs7168846	0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs7169888	0.84[ASN][1000 genomes]
rs7170311	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7170365	0.84[ASN][1000 genomes]
rs7170675	0.91[CHD][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs7171085	0.84[ASN][1000 genomes]
rs7177267	0.84[ASN][1000 genomes]
rs7180258	0.81[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs7181051	0.84[ASN][1000 genomes]
rs7181201	0.81[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs7181997	0.82[ASN][1000 genomes]
rs7182957	0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs7184026	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73408568	0.85[ASN][1000 genomes]
rs7494977	0.82[ASN][1000 genomes]
rs8024428	0.84[ASN][1000 genomes]
rs8025456	0.90[ASN][1000 genomes]
rs8026318	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8029155	0.91[CHD][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs8029369	0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs8030124	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8030214	0.96[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.89[MKK][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8031702	0.91[CHD][hapmap];0.95[JPT][hapmap];0.86[YRI][hapmap];0.82[ASN][1000 genomes]
rs8033934	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8035358	0.95[CEU][hapmap];0.86[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 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	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
5	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
6	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
7	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
8	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
9	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
10	nsv471243	chr15:51345485-52018096	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
11	esv2757600	chr15:51352249-51783981	Weak transcription Bivalent Enhancer Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6493476	GABPB1	cis	parietal	SCAN

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:51344600-51384400	Weak transcription	Brain Cingulate Gyrus	brain
2	chr15:51350400-51367600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr15:51350600-51369600	Weak transcription	HUVEC	blood vessel
4	chr15:51357800-51368400	Weak transcription	Ovary	ovary
5	chr15:51362800-51367400	Weak transcription	HSMMtube	muscle
6	chr15:51362800-51368000	Weak transcription	HSMM	muscle
7	chr15:51363800-51369000	Weak transcription	Osteobl	bone
8	chr15:51364000-51368000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr15:51364000-51368400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
10	chr15:51364000-51368400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr15:51364200-51367400	Weak transcription	NHDF-Ad	bronchial
12	chr15:51364200-51368400	Weak transcription	GM12878-XiMat	blood
13	chr15:51366000-51369200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr15:51366400-51367800	Enhancers	Adipose Nuclei	Adipose
15	chr15:51366400-51367800	Enhancers	Aorta	Aorta
16	chr15:51366600-51368000	Enhancers	Esophagus	oesophagus
17	chr15:51366600-51368600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr15:51366600-51369400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr15:51366800-51367600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr15:51366800-51367600	Enhancers	HMEC	breast
21	chr15:51366800-51367800	Enhancers	Left Ventricle	heart
22	chr15:51366800-51368800	Enhancers	Colon Smooth Muscle	Colon
23	chr15:51366800-51369000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr15:51366800-51369600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr15:51366800-51369600	Enhancers	Right Ventricle	heart
26	chr15:51366800-51370800	Enhancers	Spleen	Spleen
27	chr15:51367000-51367800	Enhancers	Pancreas	Pancrea
28	chr15:51367000-51368000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr15:51367000-51368000	Enhancers	Stomach Smooth Muscle	stomach
30	chr15:51367000-51368600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr15:51367000-51369000	Enhancers	Muscle Satellite Cultured Cells	--
32	chr15:51367000-51369200	Enhancers	Skeletal Muscle Female	skeletal muscle
33	chr15:51367200-51367600	Enhancers	NHEK	skin
34	chr15:51367200-51368400	Weak transcription	Right Atrium	heart
35	chr15:51367200-51369400	Enhancers	Skeletal Muscle Male	skeletal muscle

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