Variant report

Variant	rs12409909
Chromosome Location	chr1:59354275-59354276
allele	A/C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:59244354..59252225-chr1:59338738..59357283,49	K562	blood:
2	chr1:59242511..59252251-chr1:59329388..59355607,72	K562	blood:
3	chr1:59281044..59283680-chr1:59353136..59355336,2	K562	blood:
4	chr1:59248359..59251694-chr1:59350027..59354536,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000177606	Chromatin interaction
ENSG00000234807	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10493253	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11207323	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11207325	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11207326	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11207332	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12117564	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1536159	0.80[EUR][1000 genomes]
rs17118379	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2057596	0.83[AMR][1000 genomes]
rs2953373	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs41287666	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6587841	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6658104	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6661505	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6664131	0.82[EUR][1000 genomes]
rs6681632	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6697107	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs74078024	0.82[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	nsv1005354	chr1:59283572-59535812	Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
2	nsv829959	chr1:59340330-59503085	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:59319800-59361400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr1:59344800-59356000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr1:59347000-59354800	Enhancers	NHDF-Ad	bronchial
4	chr1:59348000-59360800	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr1:59349000-59354400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr1:59350600-59354600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr1:59351000-59360800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr1:59351200-59359000	Weak transcription	Brain Substantia Nigra	brain
9	chr1:59351400-59359200	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr1:59351800-59360800	Weak transcription	Fetal Heart	heart
11	chr1:59352000-59354400	Weak transcription	HUVEC	blood vessel
12	chr1:59352000-59359000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
13	chr1:59352200-59358800	Weak transcription	Colonic Mucosa	Colon
14	chr1:59352200-59359000	Weak transcription	Fetal Muscle Trunk	muscle
15	chr1:59352400-59354600	Weak transcription	HMEC	breast
16	chr1:59352400-59360800	Weak transcription	Brain Angular Gyrus	brain
17	chr1:59352600-59354400	Weak transcription	NH-A	brain
18	chr1:59352600-59355600	Weak transcription	Duodenum Mucosa	Duodenum
19	chr1:59352600-59355600	Weak transcription	Small Intestine	intestine
20	chr1:59352800-59354600	Weak transcription	Primary T cells from cord blood	blood
21	chr1:59352800-59354600	Weak transcription	K562	blood
22	chr1:59352800-59355400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
23	chr1:59352800-59356200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr1:59352800-59358600	Weak transcription	Gastric	stomach
25	chr1:59352800-59360600	Weak transcription	Duodenum Smooth Muscle	Duodenum
26	chr1:59353000-59354600	Weak transcription	HSMM	muscle
27	chr1:59353000-59355000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
28	chr1:59353200-59354400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr1:59353200-59354400	Weak transcription	HSMMtube	muscle
30	chr1:59353200-59354400	Weak transcription	Monocytes-CD14+_RO01746	blood
31	chr1:59353200-59354600	Weak transcription	Osteobl	bone
32	chr1:59353200-59356000	Weak transcription	Stomach Mucosa	stomach
33	chr1:59353400-59354400	Weak transcription	Primary monocytes fromperipheralblood	blood
34	chr1:59353400-59354400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr1:59353400-59355000	Enhancers	NHEK	skin
36	chr1:59353400-59355600	Weak transcription	HepG2	liver
37	chr1:59353400-59360000	Weak transcription	Colon Smooth Muscle	Colon
38	chr1:59353400-59360800	Weak transcription	Muscle Satellite Cultured Cells	--
39	chr1:59353600-59354600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr1:59353600-59354600	Weak transcription	Skeletal Muscle Female	skeletal muscle
41	chr1:59353600-59354600	Weak transcription	NHLF	lung
42	chr1:59353600-59355000	Weak transcription	Fetal Thymus	thymus
43	chr1:59353600-59355000	Weak transcription	Right Ventricle	heart
44	chr1:59353600-59355800	Weak transcription	Rectal Mucosa Donor 31	rectum
45	chr1:59353600-59359000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
46	chr1:59353600-59359000	Weak transcription	Fetal Lung	lung
47	chr1:59353600-59361200	Weak transcription	Ovary	ovary
48	chr1:59353800-59354400	Weak transcription	Right Atrium	heart
49	chr1:59353800-59354800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
50	chr1:59353800-59355800	Weak transcription	Esophagus	oesophagus

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