Variant report

Variant	rs2747042
Chromosome Location	chr1:94281678-94281679
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:94145260..94147356-chr1:94280674..94282798,2	MCF-7	breast:
2	chr1:94280000..94282465-chr1:94282888..94285001,2	K562	blood:
3	chr1:94279220..94281682-chr1:94312143..94314528,3	K562	blood:

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

Extended variants
information (count: 47 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10874797	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11164970	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11164973	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11164974	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11165022	0.82[CEU][hapmap]
rs11582870	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1884019	1.00[ASW][hapmap];0.96[CEU][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1980083	0.85[CHB][hapmap]
rs2092700	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2235970	0.84[JPT][hapmap]
rs2301022	0.94[JPT][hapmap]
rs2391315	0.85[CEU][hapmap]
rs2391321	0.85[CEU][hapmap]
rs2747036	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2747037	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2747038	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2747040	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2747044	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2747047	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2747049	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2818161	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2818165	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2818166	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2818167	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3789453	0.80[GIH][hapmap];0.94[JPT][hapmap]
rs3789457	1.00[JPT][hapmap]
rs4520428	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.98[GIH][hapmap];0.95[LWK][hapmap];0.91[MEX][hapmap];0.97[MKK][hapmap];0.98[TSI][hapmap];0.90[YRI][hapmap];0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4847184	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4847192	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4847254	0.83[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs4847257	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6541399	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6660210	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6667986	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6681265	0.81[CEU][hapmap]
rs6703684	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs743110	0.83[GIH][hapmap];0.94[JPT][hapmap]
rs7523787	0.96[CEU][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7526082	0.80[ASN][1000 genomes]
rs7552293	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs947343	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2747042	RP11-488P3.1	cis	Esophagus Muscularis	GTEx
rs2747042	RP11-488P3.1	cis	Heart Left Ventricle	GTEx
rs2747042	RP11-488P3.1	cis	Adipose Subcutaneous	GTEx
rs2747042	RP11-488P3.1	cis	Skin Sun Exposed Lower leg	GTEx
rs2747042	RP11-488P3.1	cis	Muscle Skeletal	GTEx

Chromatin state (count:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:94273600-94282800	Weak transcription	Lung	lung
2	chr1:94275800-94282400	Enhancers	Muscle Satellite Cultured Cells	--
3	chr1:94275800-94284200	Enhancers	Hela-S3	cervix
4	chr1:94275800-94285000	Enhancers	HMEC	breast
5	chr1:94276000-94283600	Enhancers	HSMM	muscle
6	chr1:94276000-94285200	Enhancers	Placenta	Placenta
7	chr1:94276800-94283800	Enhancers	NHEK	skin
8	chr1:94277000-94282400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr1:94277000-94284400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr1:94277000-94285000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr1:94277200-94282600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr1:94277600-94284600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr1:94277800-94282600	Weak transcription	Fetal Stomach	stomach
14	chr1:94278200-94282600	Weak transcription	Skeletal Muscle Male	skeletal muscle
15	chr1:94278200-94282800	Weak transcription	Right Ventricle	heart
16	chr1:94278600-94281800	Enhancers	ES-I3 Cell Line	embryonic stem cell
17	chr1:94278600-94283200	Enhancers	Osteobl	bone
18	chr1:94278600-94284000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr1:94278800-94282000	Enhancers	Placenta Amnion	Placenta Amnion
20	chr1:94278800-94282600	Weak transcription	Left Ventricle	heart
21	chr1:94279200-94281800	Enhancers	iPS-20b Cell Line	embryonic stem cell
22	chr1:94279400-94281800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr1:94279400-94282400	Enhancers	Primary hematopoietic stem cells short term culture	blood
24	chr1:94279400-94282800	Weak transcription	Duodenum Mucosa	Duodenum
25	chr1:94279400-94284400	Enhancers	Breast Myoepithelial Primary Cells	Breast
26	chr1:94279600-94282400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
27	chr1:94279600-94282400	Weak transcription	Duodenum Smooth Muscle	Duodenum
28	chr1:94279600-94282400	Weak transcription	Fetal Intestine Small	intestine
29	chr1:94279600-94282400	Weak transcription	NHDF-Ad	bronchial
30	chr1:94279600-94282600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr1:94279600-94302800	Weak transcription	Stomach Smooth Muscle	stomach
32	chr1:94279800-94282400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr1:94279800-94282400	Weak transcription	HepG2	liver
34	chr1:94279800-94282600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr1:94279800-94282600	Weak transcription	NHLF	lung
36	chr1:94279800-94284400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
37	chr1:94279800-94284600	Enhancers	Primary hematopoietic stem cells	blood
38	chr1:94280000-94282200	Weak transcription	Adipose Nuclei	Adipose
39	chr1:94280000-94282400	Weak transcription	Liver	Liver
40	chr1:94280000-94282400	Weak transcription	Fetal Thymus	thymus
41	chr1:94280000-94282600	Weak transcription	Skeletal Muscle Female	skeletal muscle
42	chr1:94280000-94282800	Weak transcription	Fetal Intestine Large	intestine
43	chr1:94280000-94285600	Weak transcription	H9 Cell Line	embryonic stem cell
44	chr1:94280000-94290000	Weak transcription	Brain Angular Gyrus	brain
45	chr1:94280200-94282200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr1:94280200-94282400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr1:94280200-94282400	Weak transcription	Right Atrium	heart
48	chr1:94280200-94284000	Weak transcription	Brain Hippocampus Middle	brain
49	chr1:94280400-94282800	Weak transcription	Fetal Muscle Trunk	muscle
50	chr1:94280400-94285000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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