Variant report

Variant	rs9524551
Chromosome Location	chr13:95246883-95246884
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr13:95246267..95250128-chr13:95251933..95256020,6	MCF-7	breast:
2	chr13:95242101..95243874-chr13:95245900..95247690,2	K562	blood:
3	chr13:95245952..95249992-chr13:95252491..95255739,5	K562	blood:
4	chr13:95242026..95244794-chr13:95245664..95248411,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000152749	Chromatin interaction

Extended variants
information (count: 63 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs1112370	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1408999	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2275647	0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[ASN][1000 genomes]
rs2275648	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2298058	1.00[CHB][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs34350725	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34405130	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35253817	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs35678857	0.99[ASN][1000 genomes]
rs3742107	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3897473	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3897474	0.88[CEU][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4473052	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4489873	0.90[CHB][hapmap];0.95[JPT][hapmap];1.00[ASN][1000 genomes]
rs4608209	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4773801	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6492716	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6492717	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6492718	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7321239	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7330873	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7331814	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7339106	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7981788	0.81[CEU][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7991607	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7997035	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7997333	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7998025	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9301979	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9301981	0.96[CEU][hapmap];1.00[CHB][hapmap];0.96[JPT][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9301983	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9516434	0.85[ASN][1000 genomes]
rs9516437	0.96[CEU][hapmap];1.00[CHB][hapmap];0.96[JPT][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9516438	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9516440	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9516441	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9516443	1.00[CHB][hapmap];0.95[JPT][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9516445	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9524544	1.00[CHB][hapmap];0.89[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9524545	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9524547	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9524548	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9524549	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9524550	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9524553	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9524554	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9524555	0.80[CEU][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9524556	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9524557	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9524559	0.80[CEU][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9556402	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9556403	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs9556405	0.82[EUR][1000 genomes]
rs9561638	1.00[ASN][1000 genomes]
rs9561642	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9590037	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv34004	chr13:94906537-95392644	Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Weak transcription 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 target site	27 gene(s)	inside rSNPs	diseases
2	nsv832685	chr13:95179676-95279966	Active TSS Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
3	nsv832686	chr13:95206742-95400992	Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
4	esv3521585	chr13:95244823-95249508	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	n/a
5	esv3497281	chr13:95244835-95249503	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	n/a
6	esv3497282	chr13:95244837-95249504	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	n/a
7	esv3521596	chr13:95244837-95249504	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	n/a

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs9524551	GPR180	cis	Esophagus Mucosa	GTEx
rs9524551	GPR180	cis	Nerve Tibial	GTEx
rs9524551	GPR180	cis	Artery Tibial	GTEx
rs9524551	GPR180	cis	Adipose Subcutaneous	GTEx
rs9524551	GPR180	cis	Stomach	GTEx
rs9524551	GPR180	cis	Muscle Skeletal	GTEx
rs9524551	GPR180	cis	Skin Sun Exposed Lower leg	GTEx
rs9524551	GPR180	cis	Whole Blood	GTEx
rs9524551	GPR180	cis	lung	GTEx

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:95222000-95247200	Weak transcription	Fetal Brain Male	brain
2	chr13:95225000-95247400	Weak transcription	Fetal Brain Female	brain
3	chr13:95233200-95247000	Weak transcription	Brain Cingulate Gyrus	brain
4	chr13:95233400-95247600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr13:95234400-95247000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr13:95234600-95247200	Weak transcription	Lung	lung
7	chr13:95235200-95247000	Weak transcription	Ovary	ovary
8	chr13:95235200-95247400	Weak transcription	Gastric	stomach
9	chr13:95235600-95247000	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr13:95235600-95247400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr13:95235600-95247400	Weak transcription	Aorta	Aorta
12	chr13:95235600-95247400	Weak transcription	HSMMtube	muscle
13	chr13:95244600-95247000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr13:95244600-95247400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
15	chr13:95244800-95247000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
16	chr13:95245000-95247000	Weak transcription	Placenta	Placenta
17	chr13:95245000-95247400	Weak transcription	Fetal Muscle Trunk	muscle
18	chr13:95245400-95247200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
19	chr13:95245400-95247400	Weak transcription	Esophagus	oesophagus
20	chr13:95245600-95247000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
21	chr13:95245600-95247000	Enhancers	Primary T killer memory cells from peripheral blood	blood
22	chr13:95245800-95247000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr13:95245800-95247000	Enhancers	Primary T helper cells fromperipheralblood	blood
24	chr13:95246000-95247400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
25	chr13:95246200-95247000	Flanking Active TSS	GM12878-XiMat	blood
26	chr13:95246200-95247600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr13:95246200-95248000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr13:95246200-95248600	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr13:95246400-95247000	Weak transcription	HUES64 Cell Line	embryonic stem cell
30	chr13:95246400-95247000	Enhancers	Primary hematopoietic stem cells	blood
31	chr13:95246400-95247000	Enhancers	Rectal Mucosa Donor 31	rectum
32	chr13:95246400-95247000	Flanking Active TSS	K562	blood
33	chr13:95246400-95247000	Enhancers	Monocytes-CD14+_RO01746	blood
34	chr13:95246400-95247200	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr13:95246400-95247200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr13:95246400-95247200	Enhancers	Brain Anterior Caudate	brain
37	chr13:95246400-95247200	Enhancers	Brain Hippocampus Middle	brain
38	chr13:95246400-95247200	Enhancers	Fetal Lung	lung
39	chr13:95246400-95247200	Enhancers	Skeletal Muscle Male	skeletal muscle
40	chr13:95246400-95247200	Flanking Active TSS	HepG2	liver
41	chr13:95246400-95247400	Enhancers	Primary neutrophils fromperipheralblood	blood
42	chr13:95246400-95247400	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
43	chr13:95246400-95247400	Enhancers	Brain Angular Gyrus	brain
44	chr13:95246400-95247400	Enhancers	Brain Substantia Nigra	brain
45	chr13:95246400-95247400	Enhancers	Fetal Heart	heart
46	chr13:95246400-95247400	Enhancers	Stomach Mucosa	stomach
47	chr13:95246400-95247600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr13:95246400-95247600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr13:95246400-95247600	Enhancers	Primary monocytes fromperipheralblood	blood
50	chr13:95246400-95247600	Flanking Active TSS	Thymus	Thymus

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