Variant report

Variant	rs2747049
Chromosome Location	chr1:94265213-94265214
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:94264120..94265962-chr1:94267264..94268908,2	K562	blood:
2	chr1:94262988..94265962-chr1:94267220..94268908,3	K562	blood:
3	chr1:94242236..94243753-chr1:94263548..94266420,2	K562	blood:

Extended variants
information (count: 35 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10874797	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11164970	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11164973	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11164974	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11582870	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1884019	0.85[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs2092700	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2747036	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2747037	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2747038	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2747040	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2747042	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2747044	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2747047	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2818161	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2818165	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2818166	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2818167	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4520428	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4847184	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4847192	0.90[EUR][1000 genomes]
rs4847254	0.88[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs4847257	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6541399	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6660210	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6667986	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6703684	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7523787	0.90[EUR][1000 genomes]
rs7552293	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs947343	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9651128	0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2747049	RP11-488P3.1	cis	Muscle Skeletal	GTEx
rs2747049	RP11-488P3.1	cis	Adipose Subcutaneous	GTEx
rs2747049	RP11-488P3.1	cis	Esophagus Muscularis	GTEx
rs2747049	RP11-488P3.1	cis	Skin Sun Exposed Lower leg	GTEx
rs2747049	RP11-488P3.1	cis	Heart Left Ventricle	GTEx

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:94246800-94266600	Weak transcription	A549	lung
2	chr1:94262400-94270200	Enhancers	Hela-S3	cervix
3	chr1:94263600-94265400	Enhancers	HMEC	breast
4	chr1:94264400-94269200	Weak transcription	NHEK	skin
5	chr1:94264400-94270000	Weak transcription	Aorta	Aorta
6	chr1:94264600-94265800	Enhancers	Muscle Satellite Cultured Cells	--
7	chr1:94264600-94267800	Weak transcription	Osteobl	bone
8	chr1:94264600-94269800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr1:94264600-94270000	Weak transcription	HSMMtube	muscle
10	chr1:94264800-94267200	Weak transcription	NHLF	lung
11	chr1:94264800-94267800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr1:94264800-94267800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr1:94264800-94268000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr1:94264800-94268600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr1:94264800-94269200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr1:94264800-94269600	Weak transcription	HSMM	muscle
17	chr1:94265000-94266800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr1:94265000-94267600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr1:94265000-94267800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr1:94265000-94267800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr1:94265000-94268000	Weak transcription	NHDF-Ad	bronchial
22	chr1:94265000-94268200	Weak transcription	HUVEC	blood vessel
23	chr1:94265000-94269200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr1:94265000-94269200	Weak transcription	NH-A	brain
25	chr1:94265200-94265800	Enhancers	HepG2	liver

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