Variant report

Variant	rs3742107
Chromosome Location	chr13:95227340-95227341
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:95226835..95228844-chr13:95230634..95232226,2	K562	blood:

Extended variants
information (count: 61 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs1112370	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1408999	0.88[AMR][1000 genomes];0.93[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];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[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	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34405130	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35253817	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs35678857	0.99[ASN][1000 genomes]
rs3897473	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3897474	0.88[CEU][hapmap];0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4473052	0.87[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[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4773801	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6492716	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6492717	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6492718	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7321239	1.00[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];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7331814	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7339106	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7981788	0.81[CEU][hapmap];0.80[YRI][hapmap];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7991607	0.86[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];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7997333	0.90[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];0.97[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];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9301981	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9301983	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9516434	0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs9516437	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9516438	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9516440	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9516441	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9516443	0.95[CHB][hapmap];0.96[JPT][hapmap];0.80[YRI][hapmap];0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9516445	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9524544	1.00[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[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];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9524547	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9524548	0.96[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]
rs9524549	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]
rs9524550	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9524551	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]
rs9524553	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9524554	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9524555	0.80[CEU][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9524556	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9524557	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9524559	0.80[CEU][hapmap];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9524561	0.80[YRI][hapmap]
rs9556402	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]
rs9556403	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs9556405	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9561638	1.00[ASN][1000 genomes]
rs9561642	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9590037	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[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:9)

SNP	Gene	Cis/trans	Tissue	Source
rs3742107	GPR180	cis	Stomach	GTEx
rs3742107	GPR180	cis	lung	GTEx
rs3742107	GPR180	cis	Nerve Tibial	GTEx
rs3742107	GPR180	cis	Skin Sun Exposed Lower leg	GTEx
rs3742107	GPR180	cis	Whole Blood	GTEx
rs3742107	GPR180	cis	Muscle Skeletal	GTEx
rs3742107	GPR180	cis	Adipose Subcutaneous	GTEx
rs3742107	GPR180	cis	Artery Tibial	GTEx
rs3742107	GPR180	cis	Esophagus Mucosa	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:95215000-95235400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr13:95218400-95232800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr13:95219200-95238200	Strong transcription	Primary T cells from cord blood	blood
4	chr13:95219600-95237000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr13:95219600-95245600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
6	chr13:95220600-95227800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr13:95220800-95227800	Strong transcription	Thymus	Thymus
8	chr13:95220800-95229200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr13:95220800-95231000	Strong transcription	Liver	Liver
10	chr13:95220800-95237000	Strong transcription	GM12878-XiMat	blood
11	chr13:95220800-95237600	Strong transcription	Fetal Intestine Large	intestine
12	chr13:95221000-95237000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr13:95221000-95238000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr13:95221000-95240000	Strong transcription	Fetal Thymus	thymus
15	chr13:95221000-95241000	Strong transcription	Dnd41	blood
16	chr13:95221200-95235600	Strong transcription	Adipose Nuclei	Adipose
17	chr13:95221200-95236600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
18	chr13:95221200-95237400	Strong transcription	Duodenum Mucosa	Duodenum
19	chr13:95221200-95238000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr13:95221200-95239200	Weak transcription	Brain Germinal Matrix	brain
21	chr13:95221400-95228000	Strong transcription	Fetal Muscle Leg	muscle
22	chr13:95221400-95235400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr13:95221400-95237400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr13:95221400-95242800	Strong transcription	Primary T helper cells fromperipheralblood	blood
25	chr13:95221400-95245800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
26	chr13:95221600-95240000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
27	chr13:95221800-95228600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr13:95221800-95237000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr13:95221800-95239800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr13:95221800-95241200	Strong transcription	Primary T helper cells PMA-I stimulated	--
31	chr13:95222000-95228000	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr13:95222000-95230200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
33	chr13:95222000-95236000	Strong transcription	HMEC	breast
34	chr13:95222000-95237400	Strong transcription	Fetal Muscle Trunk	muscle
35	chr13:95222000-95238200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr13:95222000-95240000	Strong transcription	Primary B cells from peripheral blood	blood
37	chr13:95222000-95245000	Strong transcription	Monocytes-CD14+_RO01746	blood
38	chr13:95222000-95247200	Weak transcription	Fetal Brain Male	brain
39	chr13:95222200-95229200	Strong transcription	Muscle Satellite Cultured Cells	--
40	chr13:95222200-95229200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
41	chr13:95222200-95235000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr13:95222200-95237400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr13:95222200-95239200	Strong transcription	Primary T cells fromperipheralblood	blood
44	chr13:95222200-95245000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr13:95222200-95245200	Strong transcription	Primary monocytes fromperipheralblood	blood
46	chr13:95222400-95227800	Strong transcription	Skeletal Muscle Male	skeletal muscle
47	chr13:95222400-95229600	Strong transcription	Primary neutrophils fromperipheralblood	blood
48	chr13:95222400-95229800	Strong transcription	Fetal Lung	lung
49	chr13:95222400-95230000	Strong transcription	Duodenum Smooth Muscle	Duodenum
50	chr13:95222400-95237000	Strong transcription	Rectal Mucosa Donor 31	rectum

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