Variant report

Variant	rs2747045
Chromosome Location	chr1:94277595-94277596
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:94146662..94149106-chr1:94275928..94279554,4	MCF-7	breast:
2	chr1:94146643..94149409-chr1:94276998..94280390,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000137936	Chromatin interaction

Extended variants
information (count: 65 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs10489602	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10489603	0.81[CEU][hapmap]
rs10489604	0.96[CEU][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10782966	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10782967	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11165020	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11165022	0.83[JPT][hapmap]
rs11165024	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11165026	0.83[JPT][hapmap]
rs12027630	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12041975	0.83[JPT][hapmap]
rs12122113	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12123957	0.82[EUR][1000 genomes]
rs12134359	0.92[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12137687	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12140446	0.96[CEU][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs12143274	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12143279	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12563731	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12565614	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12566531	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12734571	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12739186	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12745990	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1398798	0.88[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1884018	1.00[CEU][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1980083	0.86[CEU][hapmap]
rs2143990	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2143992	0.83[JPT][hapmap]
rs2235971	0.96[CEU][hapmap];0.95[JPT][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2391315	0.90[CHB][hapmap];0.87[JPT][hapmap]
rs2391322	0.88[CEU][hapmap];0.95[JPT][hapmap]
rs2747039	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2747041	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2747043	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2747050	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2818160	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2818162	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2818164	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2818169	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3000471	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3747965	0.96[CEU][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4075523	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4141736	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4141737	0.96[CEU][hapmap];0.95[JPT][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4240955	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4240956	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4314890	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4350209	0.83[JPT][hapmap];1.00[YRI][hapmap];0.88[EUR][1000 genomes]
rs4847253	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4847256	0.82[CEU][hapmap]
rs4847264	0.83[JPT][hapmap]
rs6663218	0.82[JPT][hapmap]
rs6664719	0.96[CEU][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6681265	0.82[JPT][hapmap]
rs6685747	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7364910	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs743111	0.82[JPT][hapmap]
rs8179391	0.80[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs871854	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv546822	chr1:94246577-94289863	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers	Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	esv1815663	chr1:94246577-94291252	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Genic enhancers	Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv1877	chr1:94247756-94292908	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Active TSS	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv508415	chr1:94256122-94305339	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription Bivalent Enhancer	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
5	esv1802380	chr1:94272119-94291252	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs2747045	RP11-488P3.1	cis	Artery Tibial	GTEx
rs2747045	RP11-488P3.1	cis	Thyroid	GTEx
rs2747045	RP11-488P3.1	cis	Stomach	GTEx
rs2747045	RP11-488P3.1	cis	Muscle Skeletal	GTEx
rs2747045	RP11-488P3.1	cis	lung	GTEx
rs2747045	RP11-488P3.1	cis	Skin Sun Exposed Lower leg	GTEx
rs2747045	RP11-488P3.1	cis	Esophagus Muscularis	GTEx
rs2747045	RP11-488P3.1	cis	Adipose Subcutaneous	GTEx
rs2747045	RP11-488P3.1	cis	Heart Left Ventricle	GTEx
rs2747045	RP11-488P3.1	cis	Nerve Tibial	GTEx

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:94271000-94279200	Weak transcription	Adipose Nuclei	Adipose
2	chr1:94271200-94278200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr1:94273600-94278600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr1:94273600-94282800	Weak transcription	Lung	lung
5	chr1:94274200-94278200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
6	chr1:94274800-94279400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
7	chr1:94275400-94279600	Enhancers	NHDF-Ad	bronchial
8	chr1:94275400-94280200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr1:94275400-94281400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr1:94275600-94277600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr1:94275800-94280200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr1:94275800-94282400	Enhancers	Muscle Satellite Cultured Cells	--
13	chr1:94275800-94284200	Enhancers	Hela-S3	cervix
14	chr1:94275800-94285000	Enhancers	HMEC	breast
15	chr1:94276000-94277600	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr1:94276000-94278200	Enhancers	Right Atrium	heart
17	chr1:94276000-94278600	Enhancers	Fetal Lung	lung
18	chr1:94276000-94281400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr1:94276000-94283600	Enhancers	HSMM	muscle
20	chr1:94276000-94285200	Enhancers	Placenta	Placenta
21	chr1:94276200-94277600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr1:94276400-94278000	Weak transcription	Skeletal Muscle Female	skeletal muscle
23	chr1:94276400-94278600	Weak transcription	NHLF	lung
24	chr1:94276600-94277600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr1:94276600-94278200	Enhancers	Fetal Muscle Leg	muscle
26	chr1:94276600-94278200	Enhancers	Right Ventricle	heart
27	chr1:94276600-94278800	Enhancers	Left Ventricle	heart
28	chr1:94276800-94277600	Enhancers	Aorta	Aorta
29	chr1:94276800-94283800	Enhancers	NHEK	skin
30	chr1:94277000-94277800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr1:94277000-94277800	Enhancers	Fetal Stomach	stomach
32	chr1:94277000-94278200	Enhancers	Fetal Brain Male	brain
33	chr1:94277000-94278200	Enhancers	Rectal Smooth Muscle	rectum
34	chr1:94277000-94282400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr1:94277000-94284400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr1:94277000-94285000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr1:94277200-94277600	Enhancers	HUVEC	blood vessel
38	chr1:94277200-94278600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
39	chr1:94277200-94280000	Weak transcription	Fetal Brain Female	brain
40	chr1:94277200-94282600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr1:94277400-94277600	Enhancers	Fetal Kidney	kidney
42	chr1:94277400-94278000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr1:94277400-94278600	Weak transcription	Osteobl	bone
44	chr1:94277400-94278800	Weak transcription	Placenta Amnion	Placenta Amnion
45	chr1:94277400-94278800	Weak transcription	HSMMtube	muscle
46	chr1:94277400-94278800	Weak transcription	NH-A	brain
47	chr1:94277400-94279400	Weak transcription	HUES6 Cell Line	embryonic stem cell

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