Variant report

Variant	rs28470464
Chromosome Location	chr18:12375871-12375872
allele	C/G
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:23)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:23 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:28974803..28975435-chr18:12375058..12375922,2	Hela-S3	cervix:
2	chr18:12361778..12363589-chr18:12374955..12376889,2	K562	blood:
3	chr18:12311231..12313531-chr18:12374709..12376964,3	K562	blood:
4	chr18:12305136..12307294-chr18:12373188..12375992,2	K562	blood:
5	chr18:12375314..12379217-chr18:12700733..12704866,11	K562	blood:
6	chr18:12358323..12362507-chr18:12375018..12379122,7	K562	blood:
7	chr18:12375743..12378274-chr18:12418543..12422031,3	MCF-7	breast:
8	chr18:12373949..12376848-chr18:12946851..12949234,5	K562	blood:
9	chr18:12375474..12376315-chr6:44214105..44215049,2	Hela-S3	cervix:
10	chr18:12374049..12378632-chr18:12655494..12660049,8	K562	blood:
11	chr18:12374593..12378692-chr18:12406477..12410976,5	K562	blood:
12	chr18:12375261..12378325-chr18:12405563..12409497,4	MCF-7	breast:
13	chr18:12375798..12379149-chr18:12946624..12949226,4	MCF-7	breast:
14	chr18:12375564..12378929-chr18:12655169..12659722,7	MCF-7	breast:
15	chr18:12372972..12377735-chr18:12656683..12660675,6	K562	blood:
16	chr18:12375835..12378198-chr18:12677932..12680535,3	K562	blood:
17	chr18:12305251..12310573-chr18:12373540..12378768,12	K562	blood:
18	chr18:12373949..12378992-chr18:12946352..12949410,8	K562	blood:
19	chr18:12307869..12309956-chr18:12375801..12377728,3	MCF-7	breast:
20	chr18:12375309..12380137-chr18:12701387..12704274,11	K562	blood:
21	chr18:12375685..12377446-chr18:12655932..12658656,3	MCF-7	breast:
22	chr18:12375636..12378066-chr18:12991064..12992748,2	K562	blood:
23	chr16:771026..772819-chr18:12375664..12378170,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000128789	Chromatin interaction
ENSG00000270103	Chromatin interaction
ENSG00000141385	Chromatin interaction
ENSG00000176014	Chromatin interaction
ENSG00000103254	Chromatin interaction
ENSG00000096384	Chromatin interaction
ENSG00000134278	Chromatin interaction
ENSG00000085415	Chromatin interaction
ENSG00000266969	Chromatin interaction
ENSG00000101639	Chromatin interaction
ENSG00000141391	Chromatin interaction
ENSG00000101624	Chromatin interaction
ENSG00000215527	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs11661684	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11661708	0.94[ASN][1000 genomes]
rs11872615	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12327346	0.93[ASN][1000 genomes]
rs28823942	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3819091	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6416994	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7231304	0.84[ASN][1000 genomes]
rs7233290	0.84[ASN][1000 genomes]
rs7235929	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7237135	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72875309	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9944742	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9946108	0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9950665	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9964041	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9964437	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9964720	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9966470	0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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	nsv909400	chr18:12201374-12585545	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
4	esv2758471	chr18:12240681-12499525	Flanking Active TSS Strong transcription ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Active TSS Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
5	esv2758714	chr18:12240681-12499525	Flanking Active TSS Weak transcription Strong transcription Active TSS Bivalent Enhancer Genic enhancers Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
6	nsv576496	chr18:12247872-12490502	Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
7	nsv1060808	chr18:12302792-12514417	Genic enhancers Weak transcription Enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
8	nsv1060728	chr18:12364077-12410409	Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:12359200-12376000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr18:12367600-12376000	Weak transcription	Fetal Kidney	kidney
3	chr18:12369400-12376000	Weak transcription	Primary neutrophils fromperipheralblood	blood
4	chr18:12370800-12376000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
5	chr18:12371000-12376000	Enhancers	Primary T helper cells fromperipheralblood	blood
6	chr18:12371000-12376000	Enhancers	Fetal Thymus	thymus
7	chr18:12371200-12376000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
8	chr18:12371400-12376000	Enhancers	Primary T helper cells PMA-I stimulated	--
9	chr18:12371400-12376000	Enhancers	Primary T killer memory cells from peripheral blood	blood
10	chr18:12371400-12376000	Enhancers	Stomach Mucosa	stomach
11	chr18:12371400-12376200	Enhancers	Primary T helper naive cells from peripheral blood	blood
12	chr18:12372400-12376000	Enhancers	Brain Hippocampus Middle	brain
13	chr18:12372600-12376000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr18:12373000-12376000	Enhancers	Brain Angular Gyrus	brain
15	chr18:12373400-12376000	Weak transcription	Pancreatic Islets	Pancreatic Islet
16	chr18:12373800-12376400	Weak transcription	Aorta	Aorta
17	chr18:12374200-12376000	Enhancers	Primary T cells fromperipheralblood	blood
18	chr18:12374400-12376000	Enhancers	Brain Cingulate Gyrus	brain
19	chr18:12374400-12376200	Enhancers	Fetal Brain Male	brain
20	chr18:12374600-12376000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
21	chr18:12374600-12376000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
22	chr18:12374600-12376000	Weak transcription	Primary hematopoietic stem cells	blood
23	chr18:12374800-12376000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
24	chr18:12374800-12376000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr18:12374800-12376000	Enhancers	Brain Inferior Temporal Lobe	brain
26	chr18:12374800-12376200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr18:12375000-12376000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr18:12375000-12376200	Enhancers	Primary B cells from peripheral blood	blood
29	chr18:12375000-12376200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
30	chr18:12375000-12376200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
31	chr18:12375000-12376200	Enhancers	Spleen	Spleen
32	chr18:12375000-12378000	Active TSS	HSMM	muscle
33	chr18:12375200-12376000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
34	chr18:12375200-12376000	Active TSS	Rectal Smooth Muscle	rectum
35	chr18:12375200-12376200	Enhancers	Primary B cells from cord blood	blood
36	chr18:12375200-12376200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr18:12375200-12376600	Flanking Active TSS	Dnd41	blood
38	chr18:12375200-12376800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr18:12375200-12376800	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
40	chr18:12375200-12378200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr18:12375200-12378400	Active TSS	ES-I3 Cell Line	embryonic stem cell
42	chr18:12375200-12378400	Active TSS	iPS-15b Cell Line	embryonic stem cell
43	chr18:12375200-12378400	Active TSS	iPS-20b Cell Line	embryonic stem cell
44	chr18:12375400-12376000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr18:12375400-12376000	Enhancers	Brain Substantia Nigra	brain
46	chr18:12375400-12376000	Active TSS	Colonic Mucosa	Colon
47	chr18:12375400-12376000	Enhancers	Esophagus	oesophagus
48	chr18:12375400-12376000	Enhancers	Lung	lung
49	chr18:12375400-12376000	Active TSS	Right Atrium	heart
50	chr18:12375400-12376000	Active TSS	HSMMtube	muscle

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