Variant report

Variant	rs12406439
Chromosome Location	chr1:103240351-103240352
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 40 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10430072	0.80[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10735776	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10747431	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10782909	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10782910	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10874660	0.80[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10874661	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12132471	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12133652	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12136992	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12144719	0.96[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12404334	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12410008	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1318755	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1599703	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1599706	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1839632	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1932341	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2086014	0.80[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2376259	0.80[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs34689850	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4590689	0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4908262	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61812153	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6577334	0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs713162	0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7521799	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs921416	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9787064	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv462705	chr1:103123803-103267759	Active TSS Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
2	nsv546923	chr1:103123803-103267759	Enhancers Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
3	nsv870987	chr1:103155901-103267759	Enhancers Active TSS ZNF genes & repeats Weak transcription Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
4	nsv462716	chr1:103176592-103259724	Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
5	nsv546924	chr1:103176592-103259724	Active TSS Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
6	nsv546925	chr1:103176592-103267759	Weak transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
7	nsv546926	chr1:103183066-103267759	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
8	nsv830882	chr1:103192683-103355802	Weak transcription Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
9	nsv546927	chr1:103199589-103267759	Active TSS Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
10	esv3403184	chr1:103238964-103241087	Active TSS Flanking Active TSS Enhancers Weak transcription	n/a	n/a	inside rSNPs	diseases
11	esv3355649	chr1:103239464-103240612	Active TSS Flanking Active TSS Enhancers Weak transcription	n/a	n/a	inside rSNPs	diseases

No data

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:103233200-103243200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr1:103238600-103241600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
3	chr1:103240000-103240800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr1:103240000-103240800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr1:103240000-103241000	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr1:103240200-103240400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr1:103240200-103240600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr1:103240200-103240600	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr1:103240200-103240600	Active TSS	Brain Hippocampus Middle	brain
10	chr1:103240200-103240600	Active TSS	Brain Inferior Temporal Lobe	brain
11	chr1:103240200-103240600	Active TSS	Brain Substantia Nigra	brain
12	chr1:103240200-103240600	Active TSS	Psoas Muscle	Psoas
13	chr1:103240200-103240600	Active TSS	Skeletal Muscle Male	skeletal muscle
14	chr1:103240200-103240600	Active TSS	Hela-S3	cervix
15	chr1:103240200-103240600	Active TSS	HMEC	breast
16	chr1:103240200-103240600	Active TSS	HSMMtube	muscle
17	chr1:103240200-103240600	Active TSS	HUVEC	blood vessel
18	chr1:103240200-103240800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr1:103240200-103240800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr1:103240200-103240800	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr1:103240200-103240800	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr1:103240200-103240800	Active TSS	Muscle Satellite Cultured Cells	--
23	chr1:103240200-103240800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr1:103240200-103240800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr1:103240200-103240800	Active TSS	Brain Angular Gyrus	brain
26	chr1:103240200-103240800	Active TSS	Fetal Muscle Leg	muscle
27	chr1:103240200-103240800	Active TSS	Ovary	ovary
28	chr1:103240200-103240800	Active TSS	Rectal Mucosa Donor 29	rectum
29	chr1:103240200-103240800	Active TSS	Rectal Smooth Muscle	rectum
30	chr1:103240200-103240800	Active TSS	Stomach Smooth Muscle	stomach
31	chr1:103240200-103240800	Active TSS	A549	lung
32	chr1:103240200-103240800	Active TSS	HSMM	muscle
33	chr1:103240200-103240800	Active TSS	Osteobl	bone
34	chr1:103240200-103241000	Active TSS	Duodenum Smooth Muscle	Duodenum

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