Variant report

Variant	rs12592277
Chromosome Location	chr15:49728759-49728760
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 62 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs1023683	0.81[AFR][1000 genomes]
rs10519226	0.80[LWK][hapmap];0.94[MKK][hapmap];0.84[AFR][1000 genomes]
rs10519227	0.95[GIH][hapmap];0.91[LWK][hapmap];1.00[MKK][hapmap];0.88[TSI][hapmap];0.91[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11630318	0.81[EUR][1000 genomes]
rs11632575	0.85[EUR][1000 genomes]
rs11633282	0.84[EUR][1000 genomes]
rs11634636	0.81[EUR][1000 genomes]
rs11635005	0.81[EUR][1000 genomes]
rs11635308	0.82[LWK][hapmap];0.97[MKK][hapmap];0.80[TSI][hapmap];0.91[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs11635354	0.88[EUR][1000 genomes]
rs11638314	0.88[EUR][1000 genomes]
rs11638606	0.84[EUR][1000 genomes]
rs11639423	0.81[AFR][1000 genomes]
rs12591799	0.90[ASN][1000 genomes]
rs12592177	0.90[ASN][1000 genomes]
rs12592296	0.90[ASN][1000 genomes]
rs12594154	0.90[ASN][1000 genomes]
rs12594827	0.90[ASN][1000 genomes]
rs12595497	0.82[ASN][1000 genomes]
rs12595701	0.82[ASN][1000 genomes]
rs17396747	0.81[EUR][1000 genomes]
rs17397211	0.81[EUR][1000 genomes]
rs17400427	0.84[AFR][1000 genomes]
rs17400706	0.82[LWK][hapmap];0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17476361	0.81[EUR][1000 genomes]
rs17477722	0.94[MKK][hapmap];0.85[EUR][1000 genomes]
rs17477923	0.95[GIH][hapmap];0.82[LWK][hapmap];0.94[MKK][hapmap];0.91[YRI][hapmap];0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17478618	0.82[LWK][hapmap];1.00[MKK][hapmap];0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17479003	0.94[MKK][hapmap];0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17479205	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17479289	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34635038	0.82[ASN][1000 genomes]
rs35692325	0.81[EUR][1000 genomes]
rs3809495	0.82[ASN][1000 genomes]
rs4338740	0.93[GIH][hapmap];0.91[LWK][hapmap];1.00[MKK][hapmap];0.91[YRI][hapmap];0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs57252806	0.84[EUR][1000 genomes]
rs57749497	0.81[EUR][1000 genomes]
rs59112977	0.85[EUR][1000 genomes]
rs60594237	0.82[EUR][1000 genomes]
rs61259878	0.91[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7162633	0.83[EUR][1000 genomes]
rs7167474	0.81[EUR][1000 genomes]
rs7168316	0.98[GIH][hapmap];0.91[LWK][hapmap];1.00[MKK][hapmap];0.88[TSI][hapmap];0.91[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73394324	0.81[EUR][1000 genomes]
rs73394331	0.81[EUR][1000 genomes]
rs73394333	0.81[EUR][1000 genomes]
rs73394339	0.81[EUR][1000 genomes]
rs73394355	0.81[EUR][1000 genomes]
rs73394359	0.82[EUR][1000 genomes]
rs73396235	0.84[EUR][1000 genomes]
rs73396238	0.87[EUR][1000 genomes]
rs73398223	0.83[EUR][1000 genomes]
rs73398243	0.86[EUR][1000 genomes]
rs73398264	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73398272	0.82[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs73398276	0.81[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs73398284	0.87[AFR][1000 genomes]
rs73400205	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8027094	0.85[EUR][1000 genomes]
rs8030457	0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1039368	chr15:49566094-49764066	Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv833002	chr15:49621400-49781799	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12592277	FGF7	cis	Muscle Skeletal	GTEx

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:49716200-49732200	Transcr. at gene 5' and 3'	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
2	chr15:49716400-49737200	Transcr. at gene 5' and 3'	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr15:49718000-49731200	Weak transcription	Left Ventricle	heart
4	chr15:49719400-49731200	Weak transcription	Fetal Muscle Leg	muscle
5	chr15:49721000-49736200	Weak transcription	Right Ventricle	heart
6	chr15:49721800-49730000	Weak transcription	Primary hematopoietic stem cells	blood
7	chr15:49725400-49731000	Weak transcription	Brain Substantia Nigra	brain
8	chr15:49725400-49733800	Enhancers	Rectal Smooth Muscle	rectum
9	chr15:49726200-49732800	Enhancers	Fetal Heart	heart
10	chr15:49726400-49729400	Weak transcription	Duodenum Smooth Muscle	Duodenum
11	chr15:49726600-49729200	Enhancers	HSMM	muscle
12	chr15:49726800-49728800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr15:49726800-49731200	Weak transcription	Ovary	ovary
14	chr15:49727000-49730400	Enhancers	Colon Smooth Muscle	Colon
15	chr15:49727200-49729200	Enhancers	Fetal Lung	lung
16	chr15:49727400-49729200	Enhancers	Muscle Satellite Cultured Cells	--
17	chr15:49727800-49729000	Enhancers	HSMMtube	muscle
18	chr15:49728000-49729400	Weak transcription	NH-A	brain
19	chr15:49728200-49728800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr15:49728200-49729800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr15:49728200-49732400	Enhancers	Fetal Stomach	stomach
22	chr15:49728400-49730000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr15:49728400-49730400	Enhancers	NHLF	lung
24	chr15:49728600-49728800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr15:49728600-49728800	Enhancers	Osteobl	bone
26	chr15:49728600-49729000	Active TSS	Stomach Smooth Muscle	stomach
27	chr15:49728600-49729200	Enhancers	NHDF-Ad	bronchial

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