Variant report

Variant	rs56359953
Chromosome Location	chr18:12694994-12694995
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr18:12689483..12696263-chr18:12698961..12704404,9	MCF-7	breast:

Variant related genes	Relation type
ENSG00000128789	Chromatin interaction
ENSG00000101624	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs11874912	0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11875046	0.94[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11875203	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11875489	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11875516	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11876168	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11877349	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12185471	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2155734	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35533206	1.00[ASN][1000 genomes]
rs45460897	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55914043	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56089701	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56132337	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56152190	1.00[ASN][1000 genomes]
rs56271712	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56382499	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56392324	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56792052	1.00[ASN][1000 genomes]
rs56909423	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58011896	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61470666	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7226376	0.84[EUR][1000 genomes]
rs7243917	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7244345	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72870545	1.00[ASN][1000 genomes]
rs9646473	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[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	nsv1063125	chr18:12046892-12918251	Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	130 gene(s)	inside rSNPs	diseases
2	nsv491873	chr18:12159445-12739784	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases
3	esv3528039	chr18:12396582-12851293	Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
4	esv3528041	chr18:12396641-12851245	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
5	nsv523743	chr18:12474505-12742809	Active TSS Weak transcription Enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
6	esv1820040	chr18:12635601-12725236	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
7	esv1817845	chr18:12635601-12733705	Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
8	esv1821625	chr18:12635601-12733705	Active TSS Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
9	esv1791969	chr18:12643193-12697711	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Genic 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	13 gene(s)	inside rSNPs	diseases
10	nsv1062014	chr18:12687210-13183383	Enhancers Active TSS Weak transcription Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	101 gene(s)	inside rSNPs	diseases
11	nsv543655	chr18:12687210-13183383	Flanking Bivalent TSS/Enh Strong transcription Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	101 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:12658800-12701800	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr18:12659000-12700200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr18:12660400-12700800	Weak transcription	Fetal Brain Male	brain
4	chr18:12662800-12701600	Weak transcription	Aorta	Aorta
5	chr18:12667000-12701600	Weak transcription	Gastric	stomach
6	chr18:12672200-12701400	Weak transcription	Colonic Mucosa	Colon
7	chr18:12672400-12697200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr18:12673200-12701600	Weak transcription	Psoas Muscle	Psoas
9	chr18:12674600-12701600	Weak transcription	Right Ventricle	heart
10	chr18:12674600-12701600	Weak transcription	Small Intestine	intestine
11	chr18:12674800-12700600	Weak transcription	Brain Substantia Nigra	brain
12	chr18:12674800-12701400	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr18:12678200-12701400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr18:12678400-12696800	Weak transcription	Primary T helper cells PMA-I stimulated	--
15	chr18:12678400-12701200	Weak transcription	NH-A	brain
16	chr18:12678400-12701600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr18:12678400-12701600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr18:12678400-12701600	Weak transcription	HSMMtube	muscle
19	chr18:12679600-12696600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr18:12679600-12698400	Weak transcription	Duodenum Mucosa	Duodenum
21	chr18:12679600-12698400	Weak transcription	NHLF	lung
22	chr18:12679600-12700400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
23	chr18:12679600-12700400	Weak transcription	Colon Smooth Muscle	Colon
24	chr18:12679600-12700600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
25	chr18:12679600-12701000	Weak transcription	Primary neutrophils fromperipheralblood	blood
26	chr18:12679600-12701000	Weak transcription	Rectal Smooth Muscle	rectum
27	chr18:12679600-12701200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr18:12679600-12701600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr18:12679800-12698800	Weak transcription	Skeletal Muscle Male	skeletal muscle
30	chr18:12679800-12701000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
31	chr18:12679800-12701000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
32	chr18:12679800-12701000	Weak transcription	Muscle Satellite Cultured Cells	--
33	chr18:12680000-12695800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr18:12680000-12698800	Weak transcription	NHDF-Ad	bronchial
35	chr18:12680000-12701200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
36	chr18:12680000-12701600	Weak transcription	Esophagus	oesophagus
37	chr18:12680000-12701600	Weak transcription	Ovary	ovary
38	chr18:12680200-12696600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr18:12680200-12700800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
40	chr18:12680800-12701400	Weak transcription	Primary B cells from peripheral blood	blood
41	chr18:12681000-12696600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
42	chr18:12681000-12697000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
43	chr18:12681400-12697400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr18:12684800-12701600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr18:12685200-12701600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr18:12685400-12701400	Weak transcription	Fetal Intestine Small	intestine
47	chr18:12685600-12698600	Weak transcription	Brain Anterior Caudate	brain
48	chr18:12685600-12701400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
49	chr18:12686400-12701000	Weak transcription	Brain Hippocampus Middle	brain
50	chr18:12686800-12700800	Weak transcription	Brain Inferior Temporal Lobe	brain

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