Variant report

Variant	rs2747043
Chromosome Location	chr1:94278929-94278930
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:94094533..94095758-chr1:94278266..94279023,3	MCF-7	breast:
2	chr1:94146662..94149106-chr1:94275928..94279554,4	MCF-7	breast:
3	chr1:94093897..94096295-chr1:94277751..94279857,3	MCF-7	breast:
4	chr1:94089082..94091665-chr1:94278876..94280669,2	MCF-7	breast:
5	chr1:94146643..94149409-chr1:94276998..94280390,3	MCF-7	breast:
6	chr1:94278734..94280540-chr1:94311900..94313768,2	MCF-7	breast:
7	chr1:94137739..94141828-chr1:94278104..94280351,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000260464	Chromatin interaction
ENSG00000211575	Chromatin interaction
ENSG00000137936	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10489602	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10489604	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10782966	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10782967	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11165020	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11165024	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12027630	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12122113	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12123957	0.82[EUR][1000 genomes]
rs12134359	0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12137687	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12140446	0.80[ASN][1000 genomes]
rs12143274	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12143279	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[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];0.96[ASN][1000 genomes]
rs1398798	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1884018	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2143990	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2235971	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2747039	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2747041	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2747045	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];0.93[ASN][1000 genomes]
rs2818160	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2818162	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2818164	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2818169	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3000471	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3747965	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4075523	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4141736	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4141737	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4240955	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4240956	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4314890	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4350209	0.88[EUR][1000 genomes]
rs4847253	0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6664719	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6685747	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7364910	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs8179391	0.80[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs871854	0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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
6	esv1822452	chr1:94278128-94320233	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	121 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs2747043	RP11-488P3.1	cis	Stomach	GTEx
rs2747043	RP11-488P3.1	cis	Adipose Subcutaneous	GTEx
rs2747043	RP11-488P3.1	cis	Esophagus Muscularis	GTEx
rs2747043	RP11-488P3.1	cis	Thyroid	GTEx
rs2747043	RP11-488P3.1	cis	lung	GTEx
rs2747043	RP11-488P3.1	cis	Artery Tibial	GTEx
rs2747043	RP11-488P3.1	cis	Skin Sun Exposed Lower leg	GTEx
rs2747043	RP11-488P3.1	cis	Nerve Tibial	GTEx
rs2747043	RP11-488P3.1	cis	Heart Left Ventricle	GTEx
rs2747043	RP11-488P3.1	cis	Muscle Skeletal	GTEx

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:94271000-94279200	Weak transcription	Adipose Nuclei	Adipose
2	chr1:94273600-94282800	Weak transcription	Lung	lung
3	chr1:94274800-94279400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
4	chr1:94275400-94279600	Enhancers	NHDF-Ad	bronchial
5	chr1:94275400-94280200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr1:94275400-94281400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr1:94275800-94280200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr1:94275800-94282400	Enhancers	Muscle Satellite Cultured Cells	--
9	chr1:94275800-94284200	Enhancers	Hela-S3	cervix
10	chr1:94275800-94285000	Enhancers	HMEC	breast
11	chr1:94276000-94281400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr1:94276000-94283600	Enhancers	HSMM	muscle
13	chr1:94276000-94285200	Enhancers	Placenta	Placenta
14	chr1:94276800-94283800	Enhancers	NHEK	skin
15	chr1:94277000-94282400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr1:94277000-94284400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr1:94277000-94285000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr1:94277200-94280000	Weak transcription	Fetal Brain Female	brain
19	chr1:94277200-94282600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr1:94277400-94279400	Weak transcription	HUES6 Cell Line	embryonic stem cell
21	chr1:94277600-94279400	Weak transcription	HUVEC	blood vessel
22	chr1:94277600-94284600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr1:94277800-94279600	Weak transcription	Fetal Kidney	kidney
24	chr1:94277800-94282600	Weak transcription	Fetal Stomach	stomach
25	chr1:94278000-94279200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr1:94278000-94279800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr1:94278000-94279800	Enhancers	HepG2	liver
28	chr1:94278000-94280000	Enhancers	Skeletal Muscle Female	skeletal muscle
29	chr1:94278200-94279000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr1:94278200-94279200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr1:94278200-94279800	Weak transcription	Fetal Brain Male	brain
32	chr1:94278200-94279800	Weak transcription	Fetal Muscle Leg	muscle
33	chr1:94278200-94279800	Weak transcription	Right Atrium	heart
34	chr1:94278200-94281600	Enhancers	iPS-18 Cell Line	embryonic stem cell
35	chr1:94278200-94282600	Weak transcription	Skeletal Muscle Male	skeletal muscle
36	chr1:94278200-94282800	Weak transcription	Right Ventricle	heart
37	chr1:94278400-94280800	Enhancers	A549	lung
38	chr1:94278600-94279000	Weak transcription	Fetal Lung	lung
39	chr1:94278600-94279200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr1:94278600-94279200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr1:94278600-94279800	Enhancers	NHLF	lung
42	chr1:94278600-94280000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr1:94278600-94280000	Enhancers	Liver	Liver
44	chr1:94278600-94281800	Enhancers	ES-I3 Cell Line	embryonic stem cell
45	chr1:94278600-94283200	Enhancers	Osteobl	bone
46	chr1:94278600-94284000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr1:94278800-94279400	Enhancers	Duodenum Mucosa	Duodenum
48	chr1:94278800-94279600	Enhancers	Fetal Intestine Small	intestine
49	chr1:94278800-94279600	Enhancers	Stomach Mucosa	stomach
50	chr1:94278800-94280000	Enhancers	Fetal Intestine Large	intestine

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