Variant report

Variant	rs559406
Chromosome Location	chr18:12857002-12857003
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr18:12854011..12857455-chr18:12881831..12884967,4	K562	blood:

Variant related genes	Relation type
ENSG00000175354	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs12957037	0.99[ASN][1000 genomes]
rs12971201	1.00[ASN][1000 genomes]
rs2542162	0.97[ASN][1000 genomes]
rs2847273	1.00[ASN][1000 genomes]
rs2847281	0.97[ASN][1000 genomes]
rs2852151	1.00[ASN][1000 genomes]
rs3826557	1.00[ASN][1000 genomes]
rs478582	0.99[ASN][1000 genomes]
rs4797709	0.95[ASN][1000 genomes]
rs588447	0.99[ASN][1000 genomes]
rs592390	0.96[ASN][1000 genomes]
rs641085	0.99[ASN][1000 genomes]
rs674222	1.00[ASN][1000 genomes]
rs8087237	0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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	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
3	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
4	nsv1064844	chr18:12748045-12953235	Flanking Active TSS Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	68 gene(s)	inside rSNPs	diseases
5	nsv543656	chr18:12748045-12953235	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	68 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:12829000-12861200	Weak transcription	Fetal Brain Female	brain
2	chr18:12829000-12862600	Weak transcription	Brain Germinal Matrix	brain
3	chr18:12838600-12857200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
4	chr18:12838600-12861800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr18:12838600-12862000	Weak transcription	Rectal Smooth Muscle	rectum
6	chr18:12838600-12862400	Weak transcription	NH-A	brain
7	chr18:12838600-12862600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr18:12838800-12879000	Weak transcription	Psoas Muscle	Psoas
9	chr18:12839400-12861200	Weak transcription	HUES64 Cell Line	embryonic stem cell
10	chr18:12839600-12857200	Weak transcription	Aorta	Aorta
11	chr18:12839600-12858800	Weak transcription	Adipose Nuclei	Adipose
12	chr18:12839600-12861200	Weak transcription	Brain Hippocampus Middle	brain
13	chr18:12839600-12862600	Weak transcription	HSMM	muscle
14	chr18:12840000-12863800	Weak transcription	Brain Anterior Caudate	brain
15	chr18:12840800-12858000	Weak transcription	Rectal Mucosa Donor 31	rectum
16	chr18:12841000-12859000	Weak transcription	Right Ventricle	heart
17	chr18:12841000-12863200	Weak transcription	Colonic Mucosa	Colon
18	chr18:12841400-12863400	Weak transcription	Esophagus	oesophagus
19	chr18:12843400-12857200	Weak transcription	HUES48 Cell Line	embryonic stem cell
20	chr18:12843600-12861400	Weak transcription	Fetal Heart	heart
21	chr18:12844200-12879800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr18:12844400-12862600	Weak transcription	K562	blood
23	chr18:12844600-12862400	Weak transcription	Small Intestine	intestine
24	chr18:12846200-12857200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
25	chr18:12846200-12857200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
26	chr18:12846800-12857200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
27	chr18:12846800-12857200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
28	chr18:12847200-12862600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr18:12848800-12858600	Weak transcription	Primary neutrophils fromperipheralblood	blood
30	chr18:12849000-12862600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr18:12849200-12861200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
32	chr18:12849200-12861200	Weak transcription	HMEC	breast
33	chr18:12852000-12857200	Strong transcription	Primary B cells from peripheral blood	blood
34	chr18:12852000-12858600	Strong transcription	Monocytes-CD14+_RO01746	blood
35	chr18:12852000-12861600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
36	chr18:12852000-12863200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr18:12852200-12859000	Weak transcription	Fetal Lung	lung
38	chr18:12852200-12859600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr18:12852400-12857200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
40	chr18:12852400-12861600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
41	chr18:12852400-12862600	Weak transcription	Muscle Satellite Cultured Cells	--
42	chr18:12852400-12862600	Weak transcription	Brain Cingulate Gyrus	brain
43	chr18:12852400-12863000	Weak transcription	NHLF	lung
44	chr18:12852600-12857400	Genic enhancers	Fetal Thymus	thymus
45	chr18:12853200-12857400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
46	chr18:12853400-12857200	Genic enhancers	Dnd41	blood
47	chr18:12853400-12857800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
48	chr18:12854200-12858200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr18:12854400-12857400	Strong transcription	NHEK	skin
50	chr18:12854400-12857800	Strong transcription	Fetal Stomach	stomach

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