Variant report

Variant	rs12239208
Chromosome Location	chr1:59349570-59349571
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

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	chr1:59348233..59353011-chr1:59368695..59371190,6	K562	blood:
4	chr1:59334588..59339856-chr1:59347478..59351607,5	K562	blood:
5	chr1:59271030..59273064-chr1:59348436..59350050,2	MCF-7	breast:
6	chr1:59348284..59350595-chr1:59436968..59439590,2	K562	blood:
7	chr1:59345982..59347514-chr1:59347634..59350108,2	MCF-7	breast:
8	chr1:59336458..59340838-chr1:59348278..59351607,4	K562	blood:

No data

Variant related genes	Relation type
ENSG00000177606	Chromatin interaction
ENSG00000234807	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10159430	1.00[CEU][hapmap];0.82[CHB][hapmap]
rs11207320	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11207324	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12079982	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs41287670	0.95[ASN][1000 genomes]
rs57136299	1.00[ASN][1000 genomes]
rs58692001	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59816047	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61474703	0.94[ASN][1000 genomes]
rs6667591	1.00[CEU][hapmap];0.82[CHB][hapmap]
rs6693265	1.00[CEU][hapmap]
rs72921508	1.00[ASN][1000 genomes]
rs744171	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][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:95 , 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	chr1:59341200-59350200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr1:59344800-59356000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr1:59346200-59350600	Enhancers	HepG2	liver
5	chr1:59346200-59353600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr1:59346200-59353800	Enhancers	Psoas Muscle	Psoas
7	chr1:59346400-59349800	Enhancers	HMEC	breast
8	chr1:59346400-59353400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr1:59346400-59354000	Enhancers	Fetal Intestine Small	intestine
10	chr1:59346600-59352000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr1:59346600-59352000	Enhancers	HUVEC	blood vessel
12	chr1:59346600-59354000	Enhancers	Fetal Intestine Large	intestine
13	chr1:59346800-59349800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr1:59346800-59351200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr1:59346800-59352000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
16	chr1:59346800-59353400	Enhancers	Primary monocytes fromperipheralblood	blood
17	chr1:59347000-59349600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr1:59347000-59349800	Enhancers	Osteobl	bone
19	chr1:59347000-59350000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr1:59347000-59350000	Enhancers	NHEK	skin
21	chr1:59347000-59350400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr1:59347000-59351200	Enhancers	Skeletal Muscle Male	skeletal muscle
23	chr1:59347000-59352000	Enhancers	Liver	Liver
24	chr1:59347000-59352000	Enhancers	Skeletal Muscle Female	skeletal muscle
25	chr1:59347000-59352600	Enhancers	NH-A	brain
26	chr1:59347000-59352800	Enhancers	Left Ventricle	heart
27	chr1:59347000-59353200	Enhancers	Stomach Mucosa	stomach
28	chr1:59347000-59353400	Enhancers	Muscle Satellite Cultured Cells	--
29	chr1:59347000-59353800	Enhancers	Lung	lung
30	chr1:59347000-59353800	Enhancers	Right Atrium	heart
31	chr1:59347000-59354800	Enhancers	NHDF-Ad	bronchial
32	chr1:59347200-59349600	Enhancers	HSMM	muscle
33	chr1:59347200-59349800	Enhancers	Breast Myoepithelial Primary Cells	Breast
34	chr1:59347200-59351400	Enhancers	Brain Cingulate Gyrus	brain
35	chr1:59347200-59353800	Enhancers	Sigmoid Colon	Sigmoid Colon
36	chr1:59347200-59354000	Enhancers	Pancreas	Pancrea
37	chr1:59347400-59350800	Weak transcription	Spleen	Spleen
38	chr1:59347600-59352600	Enhancers	Brain Anterior Caudate	brain
39	chr1:59347800-59352000	Enhancers	Pancreatic Islets	Pancreatic Islet
40	chr1:59347800-59352800	Enhancers	A549	lung
41	chr1:59348000-59349600	Enhancers	Brain Substantia Nigra	brain
42	chr1:59348000-59349800	Enhancers	Cortex derived primary cultured neurospheres	brain
43	chr1:59348000-59349800	Enhancers	Brain Hippocampus Middle	brain
44	chr1:59348000-59350000	Enhancers	Brain Inferior Temporal Lobe	brain
45	chr1:59348000-59351400	Enhancers	Brain Angular Gyrus	brain
46	chr1:59348000-59353000	Enhancers	Fetal Muscle Leg	muscle
47	chr1:59348000-59360800	Weak transcription	Placenta Amnion	Placenta Amnion
48	chr1:59348200-59349600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr1:59348200-59351400	Enhancers	Ovary	ovary
50	chr1:59348200-59352200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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