Variant report

Variant	rs871854
Chromosome Location	chr1:94197793-94197794
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 53 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10489602	1.00[CEU][hapmap];0.85[CHB][hapmap];0.95[JPT][hapmap];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10489603	0.91[GIH][hapmap]
rs10489604	1.00[CEU][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.87[TSI][hapmap];0.80[EUR][1000 genomes]
rs10782966	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10782967	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11165020	0.85[EUR][1000 genomes]
rs11165024	0.82[EUR][1000 genomes]
rs12027630	0.81[EUR][1000 genomes]
rs12122113	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12123957	0.82[EUR][1000 genomes]
rs12134359	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12137687	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12140446	1.00[CEU][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.85[MEX][hapmap];0.85[TSI][hapmap]
rs12143274	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12143279	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12563731	0.83[EUR][1000 genomes]
rs12565614	0.84[EUR][1000 genomes]
rs12565817	0.91[GIH][hapmap]
rs12566531	0.83[EUR][1000 genomes]
rs12734571	0.81[EUR][1000 genomes]
rs12739186	0.84[EUR][1000 genomes]
rs12745990	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1398798	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1884018	0.96[CEU][hapmap];0.91[JPT][hapmap];0.83[EUR][1000 genomes]
rs1980083	0.81[CEU][hapmap]
rs2143990	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2235971	1.00[CEU][hapmap];0.98[GIH][hapmap];0.91[JPT][hapmap];0.85[MEX][hapmap];0.87[TSI][hapmap];0.81[EUR][1000 genomes]
rs2391315	0.83[JPT][hapmap]
rs2391322	0.92[CEU][hapmap];0.95[GIH][hapmap];0.91[JPT][hapmap];0.81[MEX][hapmap]
rs2747039	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2747041	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2747043	0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2747045	0.96[CEU][hapmap];0.85[CHB][hapmap];0.95[JPT][hapmap];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2747050	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2818160	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2818162	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2818164	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2818169	0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3000471	0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3747965	1.00[CEU][hapmap];0.98[GIH][hapmap];0.91[JPT][hapmap];0.85[MEX][hapmap];0.87[TSI][hapmap];0.81[EUR][1000 genomes]
rs4075523	1.00[CEU][hapmap];0.85[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.84[MEX][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4141736	0.81[EUR][1000 genomes]
rs4141737	1.00[CEU][hapmap];0.98[GIH][hapmap];0.91[JPT][hapmap];0.85[MEX][hapmap];0.87[TSI][hapmap];0.81[EUR][1000 genomes]
rs4240955	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4240956	1.00[CEU][hapmap];0.85[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.85[MEX][hapmap];0.95[TSI][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4314890	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4350209	0.98[GIH][hapmap];0.85[MEX][hapmap];0.82[TSI][hapmap];0.84[EUR][1000 genomes]
rs4847253	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4847256	0.85[CEU][hapmap]
rs6664719	1.00[CEU][hapmap];0.98[GIH][hapmap];0.91[JPT][hapmap];0.85[MEX][hapmap];0.87[TSI][hapmap];0.80[EUR][1000 genomes]
rs6685747	0.91[EUR][1000 genomes]
rs7364910	0.84[EUR][1000 genomes]
rs8179391	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs871854	RP11-488P3.1	cis	Esophagus Muscularis	GTEx
rs871854	RP11-488P3.1	cis	Heart Left Ventricle	GTEx
rs871854	RP11-488P3.1	cis	lung	GTEx
rs871854	RP11-488P3.1	cis	Thyroid	GTEx
rs871854	RP11-488P3.1	cis	Skin Sun Exposed Lower leg	GTEx
rs871854	RP11-488P3.1	cis	Muscle Skeletal	GTEx
rs871854	RP11-488P3.1	cis	Stomach	GTEx

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:94188000-94198400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
2	chr1:94188800-94198400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr1:94189000-94200000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr1:94189600-94198200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr1:94190000-94199000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr1:94190200-94198200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr1:94190400-94199000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr1:94190600-94200800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr1:94193000-94198000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr1:94193400-94198000	Enhancers	Breast Myoepithelial Primary Cells	Breast
11	chr1:94193800-94198200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
12	chr1:94194000-94198000	Weak transcription	Primary B cells from peripheral blood	blood
13	chr1:94195200-94197800	Enhancers	Placenta	Placenta
14	chr1:94195400-94199200	Weak transcription	Brain Angular Gyrus	brain
15	chr1:94195600-94198000	Enhancers	NHEK	skin
16	chr1:94195800-94198000	Enhancers	HMEC	breast
17	chr1:94195800-94199000	Enhancers	Fetal Thymus	thymus
18	chr1:94196200-94200600	Weak transcription	Placenta Amnion	Placenta Amnion
19	chr1:94196200-94205800	Weak transcription	Brain Inferior Temporal Lobe	brain
20	chr1:94196400-94197800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr1:94196400-94198600	Enhancers	Ovary	ovary
22	chr1:94196600-94198000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr1:94196600-94200000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr1:94196600-94204000	Weak transcription	Lung	lung
25	chr1:94197200-94199800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr1:94197400-94197800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr1:94197400-94197800	Enhancers	Adipose Nuclei	Adipose
28	chr1:94197400-94197800	Enhancers	Right Atrium	heart
29	chr1:94197400-94197800	Enhancers	HSMM	muscle
30	chr1:94197400-94198000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr1:94197400-94199000	Enhancers	Fetal Muscle Leg	muscle
32	chr1:94197400-94202000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr1:94197600-94197800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr1:94197600-94197800	Enhancers	HepG2	liver
35	chr1:94197600-94198200	Weak transcription	A549	lung
36	chr1:94197600-94198400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr1:94197600-94198400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr1:94197600-94198600	Enhancers	GM12878-XiMat	blood
39	chr1:94197600-94198800	Weak transcription	Fetal Muscle Trunk	muscle
40	chr1:94197600-94200400	Weak transcription	HSMMtube	muscle
41	chr1:94197600-94200600	Weak transcription	Hela-S3	cervix
42	chr1:94197600-94201200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr1:94197600-94205800	Weak transcription	Spleen	Spleen

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