Variant report

Variant	rs1408999
Chromosome Location	chr13:95220009-95220010
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 60 )
Associated
traits (count: 14 )

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

rs_ID	r²[population]
rs1112370	0.84[CEU][hapmap];1.00[CHB][hapmap];0.84[CHD][hapmap];0.88[GIH][hapmap];0.91[JPT][hapmap];0.82[TSI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1572935	0.85[MEX][hapmap]
rs2275647	0.95[CHB][hapmap];0.81[CHD][hapmap];0.86[JPT][hapmap];0.96[ASN][1000 genomes]
rs2275648	0.88[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2298058	1.00[CHB][hapmap];0.85[JPT][hapmap];0.94[ASN][1000 genomes]
rs34350725	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34405130	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35253817	0.82[EUR][1000 genomes]
rs35678857	0.96[ASN][1000 genomes]
rs3742107	0.88[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3897473	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3897474	0.95[MEX][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4473052	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4489873	0.90[CHB][hapmap];0.86[JPT][hapmap];0.96[ASN][1000 genomes]
rs4608209	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4773801	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6492716	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6492717	0.87[ASN][1000 genomes]
rs6492718	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7321239	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7330873	1.00[CHB][hapmap];0.86[CHD][hapmap];0.84[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.82[TSI][hapmap];0.85[YRI][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7331814	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7339106	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7981788	0.81[EUR][1000 genomes]
rs7991607	0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7997035	0.88[CEU][hapmap];1.00[CHB][hapmap];0.84[CHD][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7997333	0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7998025	0.88[CEU][hapmap];1.00[CHB][hapmap];0.84[CHD][hapmap];0.87[GIH][hapmap];0.91[JPT][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9301979	0.88[CEU][hapmap];1.00[CHB][hapmap];0.84[CHD][hapmap];0.87[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9301981	0.84[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9301983	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9516434	0.82[ASN][1000 genomes]
rs9516437	0.84[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.88[YRI][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9516438	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9516440	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9516441	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9516443	0.95[CHB][hapmap];0.86[JPT][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9516445	0.82[EUR][1000 genomes]
rs9524544	1.00[CHB][hapmap];0.89[JPT][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9524545	0.88[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];0.87[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9524547	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9524548	0.85[CEU][hapmap];1.00[CHB][hapmap];0.84[CHD][hapmap];0.91[JPT][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9524549	0.88[CEU][hapmap];1.00[CHB][hapmap];0.84[CHD][hapmap];0.87[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9524550	0.88[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9524551	0.92[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9524553	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9524554	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9524555	0.83[GIH][hapmap];0.95[MEX][hapmap];0.82[EUR][1000 genomes]
rs9524556	0.82[EUR][1000 genomes]
rs9524557	0.82[EUR][1000 genomes]
rs9524559	0.83[GIH][hapmap];0.95[MEX][hapmap];0.81[EUR][1000 genomes]
rs9556402	0.88[CEU][hapmap];1.00[CHB][hapmap];0.81[CHD][hapmap];0.95[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.82[TSI][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9556403	1.00[CHB][hapmap];0.81[CHD][hapmap];0.90[JPT][hapmap];0.96[ASN][1000 genomes]
rs9561638	0.96[ASN][1000 genomes]
rs9561642	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9590037	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[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:14)

SNP	Gene	Cis/trans	Tissue	Source
rs1408999	GPR180	cis	parietal	SCAN
rs1408999	GPR180	cis	Skin Sun Exposed Lower leg	GTEx
rs1408999	GPR180	cis	Muscle Skeletal	GTEx
rs1408999	GPR180	cis	Stomach	GTEx
rs1408999	GPC5	cis	parietal	SCAN
rs1408999	GPR180	cis	Esophagus Mucosa	GTEx
rs1408999	GPR180	cis	lung	GTEx
rs1408999	GPR180	cis	Adipose Subcutaneous	GTEx
rs1408999	GPR180	cis	Nerve Tibial	GTEx
rs1408999	GPR180	cis	Whole Blood	GTEx
rs1408999	ZDHHC9	trans	parietal	SCAN
rs1408999	GPR180	cis	cerebellum	SCAN
rs1408999	GPR180	cis	Artery Tibial	GTEx
rs1408999	ITR	cis	multi-tissue	Pritchard

Chromatin state (count:92 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:95202600-95221400	Weak transcription	Gastric	stomach
2	chr13:95202800-95221400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
3	chr13:95202800-95222000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr13:95202800-95223600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr13:95203000-95221200	Weak transcription	Duodenum Mucosa	Duodenum
6	chr13:95203000-95221400	Weak transcription	Fetal Intestine Small	intestine
7	chr13:95203000-95222400	Weak transcription	HUES6 Cell Line	embryonic stem cell
8	chr13:95203200-95220800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr13:95203200-95220800	Weak transcription	Fetal Intestine Large	intestine
10	chr13:95203200-95222200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
11	chr13:95203400-95222400	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr13:95203400-95222600	Weak transcription	A549	lung
13	chr13:95209200-95221600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
14	chr13:95209200-95222600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr13:95209400-95221000	Weak transcription	Fetal Stomach	stomach
16	chr13:95209400-95225000	Weak transcription	HepG2	liver
17	chr13:95209600-95220600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr13:95209600-95222000	Weak transcription	HMEC	breast
19	chr13:95209800-95223000	Weak transcription	HUVEC	blood vessel
20	chr13:95210000-95222000	Weak transcription	Esophagus	oesophagus
21	chr13:95210000-95222000	Weak transcription	Lung	lung
22	chr13:95210200-95221200	Weak transcription	Adipose Nuclei	Adipose
23	chr13:95210600-95222000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr13:95210600-95222200	Weak transcription	Muscle Satellite Cultured Cells	--
25	chr13:95210800-95225000	Weak transcription	K562	blood
26	chr13:95211200-95221400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr13:95211200-95222000	Weak transcription	Primary B cells from peripheral blood	blood
28	chr13:95211400-95222200	Weak transcription	Primary T cells fromperipheralblood	blood
29	chr13:95211400-95223000	Weak transcription	Small Intestine	intestine
30	chr13:95211600-95221200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
31	chr13:95211800-95222400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
32	chr13:95211800-95224000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
33	chr13:95212000-95221000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
34	chr13:95212000-95221400	Weak transcription	Primary T helper cells fromperipheralblood	blood
35	chr13:95212200-95221200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr13:95212200-95221600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr13:95212200-95221600	Weak transcription	Spleen	Spleen
38	chr13:95212200-95221800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
39	chr13:95212200-95222000	Weak transcription	Pancreas	Pancrea
40	chr13:95212200-95223600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
41	chr13:95212400-95222800	Weak transcription	Skeletal Muscle Female	skeletal muscle
42	chr13:95212400-95223400	Weak transcription	HSMM	muscle
43	chr13:95212600-95220800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr13:95212600-95220800	Weak transcription	Thymus	Thymus
45	chr13:95212600-95220800	Weak transcription	GM12878-XiMat	blood
46	chr13:95212600-95221800	Weak transcription	Primary T helper cells PMA-I stimulated	--
47	chr13:95212600-95222000	Weak transcription	Left Ventricle	heart
48	chr13:95212600-95223600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
49	chr13:95212800-95225000	Weak transcription	Placenta Amnion	Placenta Amnion
50	chr13:95213000-95222000	Weak transcription	Fetal Muscle Trunk	muscle

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