Variant report

Variant	rs9301981
Chromosome Location	chr13:95250102-95250103
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	chr13:95246267..95250128-chr13:95251933..95256020,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000152749	Chromatin interaction

Extended variants
information (count: 64 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs1112370	0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1408999	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1572935	0.86[YRI][hapmap]
rs2275647	0.91[CHB][hapmap];0.90[JPT][hapmap];0.96[ASN][1000 genomes]
rs2275648	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2298055	1.00[YRI][hapmap]
rs2298057	1.00[YRI][hapmap]
rs2298058	0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs34350725	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34405130	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35253817	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs35678857	0.95[ASN][1000 genomes]
rs3742107	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]
rs3897473	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3897474	0.92[CEU][hapmap];0.92[YRI][hapmap];0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4473052	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4489873	0.85[CHB][hapmap];0.91[JPT][hapmap];0.96[ASN][1000 genomes]
rs4608209	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4771890	1.00[YRI][hapmap]
rs4773801	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6492716	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6492717	0.85[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs6492718	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7321239	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7330873	0.87[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7331814	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7339106	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7981788	0.85[CEU][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7991607	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7997035	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7997333	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7998025	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9301979	0.96[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9301983	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9516434	0.80[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs9516437	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9516438	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9516440	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9516441	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9516443	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9516445	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9524544	1.00[CHB][hapmap];0.84[JPT][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9524545	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9524547	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9524548	0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9524549	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9524550	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9524551	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]
rs9524553	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9524554	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9524555	0.84[CEU][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9524556	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9524557	0.82[CEU][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9524559	0.84[CEU][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9524561	1.00[YRI][hapmap]
rs9556402	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9556403	0.95[CHB][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs9556405	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9561638	0.96[ASN][1000 genomes]
rs9561642	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9590037	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs9301981	GPR180	cis	Adipose Subcutaneous	GTEx
rs9301981	GPR180	cis	Whole Blood	GTEx
rs9301981	GPR180	cis	Nerve Tibial	GTEx
rs9301981	GPR180	cis	Artery Tibial	GTEx
rs9301981	GPR180	cis	lung	GTEx
rs9301981	GPR180	cis	Esophagus Mucosa	GTEx
rs9301981	GPR180	cis	Skin Sun Exposed Lower leg	GTEx
rs9301981	GPR180	cis	Stomach	GTEx
rs9301981	GPR180	cis	Muscle Skeletal	GTEx

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:95248800-95253200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr13:95248800-95253200	Weak transcription	Primary T cells from cord blood	blood
3	chr13:95248800-95253600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
4	chr13:95248800-95253600	Weak transcription	HUVEC	blood vessel
5	chr13:95249000-95250200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr13:95249000-95250200	Weak transcription	NHLF	lung
7	chr13:95249000-95252000	Weak transcription	Fetal Intestine Large	intestine
8	chr13:95249000-95252000	Weak transcription	Stomach Mucosa	stomach
9	chr13:95249000-95252200	Weak transcription	Fetal Intestine Small	intestine
10	chr13:95249000-95252800	Weak transcription	GM12878-XiMat	blood
11	chr13:95249000-95253000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
12	chr13:95249000-95253200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr13:95249000-95253200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
14	chr13:95249000-95253200	Weak transcription	Primary neutrophils fromperipheralblood	blood
15	chr13:95249000-95253200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
16	chr13:95249000-95253200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
17	chr13:95249000-95253200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
18	chr13:95249000-95253200	Weak transcription	Primary T helper cells PMA-I stimulated	--
19	chr13:95249000-95253200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
20	chr13:95249000-95253200	Weak transcription	Cortex derived primary cultured neurospheres	brain
21	chr13:95249000-95253200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr13:95249000-95253200	Weak transcription	Brain Anterior Caudate	brain
23	chr13:95249000-95253200	Weak transcription	Brain Cingulate Gyrus	brain
24	chr13:95249000-95253200	Weak transcription	Brain Substantia Nigra	brain
25	chr13:95249000-95253200	Weak transcription	Colon Smooth Muscle	Colon
26	chr13:95249000-95253200	Weak transcription	Fetal Brain Male	brain
27	chr13:95249000-95253200	Weak transcription	Fetal Heart	heart
28	chr13:95249000-95253200	Weak transcription	Fetal Kidney	kidney
29	chr13:95249000-95253200	Weak transcription	Fetal Stomach	stomach
30	chr13:95249000-95253200	Weak transcription	Rectal Smooth Muscle	rectum
31	chr13:95249000-95253200	Weak transcription	Skeletal Muscle Male	skeletal muscle
32	chr13:95249000-95253200	Weak transcription	Osteobl	bone
33	chr13:95249000-95253600	Weak transcription	Primary monocytes fromperipheralblood	blood
34	chr13:95249000-95253600	Weak transcription	Primary hematopoietic stem cells	blood
35	chr13:95249000-95253600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
36	chr13:95249000-95253600	Weak transcription	Primary T helper cells fromperipheralblood	blood
37	chr13:95249000-95253600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr13:95249000-95253600	Weak transcription	Muscle Satellite Cultured Cells	--
39	chr13:95249000-95253600	Weak transcription	Adipose Nuclei	Adipose
40	chr13:95249000-95253600	Weak transcription	Fetal Muscle Trunk	muscle
41	chr13:95249000-95253600	Weak transcription	Right Atrium	heart
42	chr13:95249000-95253600	Weak transcription	Monocytes-CD14+_RO01746	blood
43	chr13:95249000-95253800	Weak transcription	Spleen	Spleen
44	chr13:95249200-95251800	Weak transcription	Liver	Liver
45	chr13:95249200-95252000	Weak transcription	HepG2	liver
46	chr13:95249200-95252400	Weak transcription	Duodenum Mucosa	Duodenum
47	chr13:95249200-95252800	Weak transcription	Primary B cells from peripheral blood	blood
48	chr13:95249200-95253000	Weak transcription	Fetal Muscle Leg	muscle
49	chr13:95249200-95253200	Weak transcription	Primary T cells fromperipheralblood	blood
50	chr13:95249200-95253200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood

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