Variant report

Variant	rs6492717
Chromosome Location	chr13:95237526-95237527
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:95236767..95238765-chr13:95240414..95242453,2	MCF-7	breast:

Extended variants
information (count: 50 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs1112370	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1408999	0.87[ASN][1000 genomes]
rs2275647	0.91[ASN][1000 genomes]
rs2275648	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2298058	0.88[ASN][1000 genomes]
rs34350725	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34405130	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35678857	0.90[ASN][1000 genomes]
rs3742107	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3897474	0.81[AMR][1000 genomes]
rs4473052	0.90[ASN][1000 genomes]
rs4489873	0.91[ASN][1000 genomes]
rs4608209	0.94[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4773801	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6492716	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6492718	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7321239	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7330873	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7331814	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7339106	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7991607	0.91[ASN][1000 genomes]
rs7997035	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7997333	0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs7998025	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9301979	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9301981	0.85[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs9301983	0.86[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs9516437	0.86[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs9516438	0.85[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs9516440	0.86[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs9516441	0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs9516443	0.86[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs9524544	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9524545	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9524547	0.85[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs9524548	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9524549	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9524550	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9524551	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9524553	0.85[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs9524554	0.86[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs9556402	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9556403	0.91[ASN][1000 genomes]
rs9561638	0.91[ASN][1000 genomes]
rs9561642	0.85[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs9590037	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[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	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	nsv562756	chr13:95178317-95238154	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
3	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
4	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

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs6492717	GPR180	cis	lung	GTEx
rs6492717	GPR180	cis	Adipose Subcutaneous	GTEx
rs6492717	GPR180	cis	Skin Sun Exposed Lower leg	GTEx
rs6492717	GPR180	cis	Artery Tibial	GTEx
rs6492717	GPR180	cis	Muscle Skeletal	GTEx
rs6492717	GPR180	cis	Whole Blood	GTEx
rs6492717	GPR180	cis	Esophagus Mucosa	GTEx
rs6492717	GPR180	cis	Nerve Tibial	GTEx

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:95219200-95238200	Strong transcription	Primary T cells from cord blood	blood
2	chr13:95219600-95245600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
3	chr13:95220800-95237600	Strong transcription	Fetal Intestine Large	intestine
4	chr13:95221000-95238000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr13:95221000-95240000	Strong transcription	Fetal Thymus	thymus
6	chr13:95221000-95241000	Strong transcription	Dnd41	blood
7	chr13:95221200-95238000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr13:95221200-95239200	Weak transcription	Brain Germinal Matrix	brain
9	chr13:95221400-95242800	Strong transcription	Primary T helper cells fromperipheralblood	blood
10	chr13:95221400-95245800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr13:95221600-95240000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
12	chr13:95221800-95239800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr13:95221800-95241200	Strong transcription	Primary T helper cells PMA-I stimulated	--
14	chr13:95222000-95238200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr13:95222000-95240000	Strong transcription	Primary B cells from peripheral blood	blood
16	chr13:95222000-95245000	Strong transcription	Monocytes-CD14+_RO01746	blood
17	chr13:95222000-95247200	Weak transcription	Fetal Brain Male	brain
18	chr13:95222200-95239200	Strong transcription	Primary T cells fromperipheralblood	blood
19	chr13:95222200-95245000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr13:95222200-95245200	Strong transcription	Primary monocytes fromperipheralblood	blood
21	chr13:95222400-95239800	Strong transcription	HUES6 Cell Line	embryonic stem cell
22	chr13:95222600-95237600	Strong transcription	H1 Cell Line	embryonic stem cell
23	chr13:95222600-95240000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
24	chr13:95222800-95239600	Strong transcription	HUES64 Cell Line	embryonic stem cell
25	chr13:95223000-95245800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
26	chr13:95224200-95246400	Weak transcription	Fetal Heart	heart
27	chr13:95224200-95246400	Weak transcription	Stomach Mucosa	stomach
28	chr13:95224400-95242800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
29	chr13:95225000-95247400	Weak transcription	Fetal Brain Female	brain
30	chr13:95225200-95242800	Weak transcription	Small Intestine	intestine
31	chr13:95226000-95245800	Weak transcription	Pancreatic Islets	Pancreatic Islet
32	chr13:95226200-95245400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr13:95226800-95246800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
34	chr13:95230400-95238200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
35	chr13:95231200-95237600	Strong transcription	Cortex derived primary cultured neurospheres	brain
36	chr13:95231200-95237800	Strong transcription	Primary hematopoietic stem cells	blood
37	chr13:95231400-95237600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr13:95231400-95237600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr13:95231600-95238000	Strong transcription	Left Ventricle	heart
40	chr13:95231800-95237600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr13:95232200-95237600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr13:95233000-95246600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
43	chr13:95233200-95242800	Weak transcription	NHEK	skin
44	chr13:95233200-95246600	Weak transcription	Placenta Amnion	Placenta Amnion
45	chr13:95233200-95247000	Weak transcription	Brain Cingulate Gyrus	brain
46	chr13:95233400-95247600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
47	chr13:95233800-95242800	Weak transcription	Brain Substantia Nigra	brain
48	chr13:95234200-95244600	Weak transcription	Esophagus	oesophagus
49	chr13:95234400-95246800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr13:95234400-95246800	Weak transcription	Brain Inferior Temporal Lobe	brain

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