Variant report

Variant	rs59459240
Chromosome Location	chr1:153797044-153797045
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:153795765..153798553-chr1:153961941..153964653,2	K562	blood:
2	chr1:153753381..153755044-chr1:153796141..153797868,2	MCF-7	breast:
3	chr1:153794811..153797634-chr1:153899769..153901924,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000177954	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs11264446	0.96[EUR][1000 genomes]
rs12032791	0.92[EUR][1000 genomes]
rs12071117	0.92[EUR][1000 genomes]
rs16835600	0.96[EUR][1000 genomes]
rs4128790	0.96[EUR][1000 genomes]
rs4845573	0.92[EUR][1000 genomes]
rs4845584	0.80[EUR][1000 genomes]
rs60341318	0.87[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs60382526	0.80[EUR][1000 genomes]
rs6666957	0.88[EUR][1000 genomes]
rs6676863	0.80[EUR][1000 genomes]
rs6693773	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72042190	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7415816	0.80[EUR][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	nsv1011897	chr1:153613597-153836703	Active TSS Genic enhancers Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
2	nsv999364	chr1:153622634-154419436	Strong transcription Genic enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	286 gene(s)	inside rSNPs	diseases
3	nsv535175	chr1:153622634-154419436	Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	286 gene(s)	inside rSNPs	diseases
4	nsv531892	chr1:153671910-153954090	Flanking Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
5	nsv464039	chr1:153708906-153801098	Genic enhancers Weak transcription Active TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
6	nsv547941	chr1:153708906-153801098	Genic enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
7	nsv817392	chr1:153724807-153870005	Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
8	nsv532551	chr1:153732039-154192279	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	233 gene(s)	inside rSNPs	diseases
9	esv1830663	chr1:153779296-153807816	Strong transcription Weak transcription Genic enhancers Enhancers Flanking Active TSS ZNF genes & repeats	Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
10	esv1825546	chr1:153779296-153821716	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS	Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
11	esv1825076	chr1:153779296-153843413	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:153774000-153801800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr1:153775000-153798800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr1:153777400-153801000	Strong transcription	Fetal Intestine Small	intestine
4	chr1:153778400-153820400	Weak transcription	Stomach Mucosa	stomach
5	chr1:153781600-153826800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr1:153786400-153811000	Weak transcription	Psoas Muscle	Psoas
7	chr1:153788200-153801600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr1:153789000-153798800	Weak transcription	Right Atrium	heart
9	chr1:153789400-153803200	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr1:153790200-153814400	Weak transcription	Small Intestine	intestine
11	chr1:153790600-153797200	Weak transcription	Esophagus	oesophagus
12	chr1:153790600-153799400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
13	chr1:153790600-153802000	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr1:153790800-153799000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr1:153790800-153799000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr1:153790800-153799000	Weak transcription	Fetal Kidney	kidney
17	chr1:153791000-153799600	Weak transcription	Brain Cingulate Gyrus	brain
18	chr1:153791400-153797200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr1:153791400-153798800	Weak transcription	Brain Germinal Matrix	brain
20	chr1:153791400-153798800	Weak transcription	Brain Inferior Temporal Lobe	brain
21	chr1:153791400-153798800	Weak transcription	Gastric	stomach
22	chr1:153791400-153798800	Weak transcription	Pancreas	Pancrea
23	chr1:153791400-153798800	Weak transcription	Right Ventricle	heart
24	chr1:153791400-153799000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr1:153791600-153797200	Weak transcription	Sigmoid Colon	Sigmoid Colon
26	chr1:153791600-153797400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
27	chr1:153791600-153797600	Weak transcription	Colon Smooth Muscle	Colon
28	chr1:153791600-153797600	Weak transcription	Skeletal Muscle Male	skeletal muscle
29	chr1:153791600-153797800	Weak transcription	Fetal Muscle Leg	muscle
30	chr1:153791600-153798000	Weak transcription	Colonic Mucosa	Colon
31	chr1:153791600-153798200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr1:153791600-153798200	Weak transcription	Skeletal Muscle Female	skeletal muscle
33	chr1:153791600-153798400	Weak transcription	Spleen	Spleen
34	chr1:153791600-153798800	Weak transcription	Left Ventricle	heart
35	chr1:153791600-153798800	Weak transcription	Rectal Mucosa Donor 31	rectum
36	chr1:153791600-153799000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
37	chr1:153791600-153799000	Weak transcription	Liver	Liver
38	chr1:153791600-153799000	Weak transcription	Duodenum Smooth Muscle	Duodenum
39	chr1:153791600-153799000	Weak transcription	NHLF	lung
40	chr1:153791600-153799200	Weak transcription	Rectal Smooth Muscle	rectum
41	chr1:153791600-153799800	Weak transcription	NH-A	brain
42	chr1:153791600-153800400	Weak transcription	Aorta	Aorta
43	chr1:153791600-153800600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr1:153791600-153822200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
45	chr1:153791800-153797400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr1:153791800-153797400	Weak transcription	Brain Substantia Nigra	brain
47	chr1:153791800-153798200	Weak transcription	Brain Hippocampus Middle	brain
48	chr1:153791800-153798800	Weak transcription	Primary hematopoietic stem cells	blood
49	chr1:153791800-153798800	Weak transcription	Stomach Smooth Muscle	stomach
50	chr1:153791800-153798800	Weak transcription	Thymus	Thymus

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