Variant report

Variant	rs55800510
Chromosome Location	chr1:154417187-154417188
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:154413948..154418058-chr1:154421616..154424516,3	MCF-7	breast:
2	chr1:154376681..154379815-chr1:154416251..154417993,3	MCF-7	breast:
3	chr1:154377603..154379181-chr1:154416383..154418263,2	MCF-7	breast:
4	chr1:154415046..154417518-chr1:154446987..154449736,2	K562	blood:
5	chr1:154409978..154411653-chr1:154414842..154417347,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000228013	Chromatin interaction
ENSG00000160712	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10159236	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11265618	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11804305	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12023358	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12047973	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12048091	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12048950	0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4308966	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4329505	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4345796	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4845626	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs55826755	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57502626	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61812592	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61812593	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61812594	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61812596	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61812599	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs61812626	0.85[EUR][1000 genomes];0.82[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	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
2	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
3	nsv948413	chr1:153974621-154797272	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	132 gene(s)	inside rSNPs	diseases
4	nsv1000402	chr1:153991106-154527053	Strong transcription Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	106 gene(s)	inside rSNPs	diseases
5	nsv521887	chr1:154236570-154684106	Strong transcription Flanking Active TSS Active TSS Weak transcription Enhancers Bivalent Enhancer Genic enhancers 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	65 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:154403200-154426000	Weak transcription	Brain Angular Gyrus	brain
2	chr1:154403800-154417600	Weak transcription	Small Intestine	intestine
3	chr1:154406000-154423200	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr1:154406200-154417600	Weak transcription	Hela-S3	cervix
5	chr1:154406200-154425600	Weak transcription	Primary B cells from cord blood	blood
6	chr1:154407400-154417400	Weak transcription	Brain Anterior Caudate	brain
7	chr1:154407600-154417200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr1:154407600-154418600	Weak transcription	Ovary	ovary
9	chr1:154408600-154420600	Weak transcription	Brain Hippocampus Middle	brain
10	chr1:154408600-154425800	Weak transcription	Brain Substantia Nigra	brain
11	chr1:154408800-154420600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr1:154408800-154420600	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr1:154408800-154421000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
14	chr1:154408800-154425600	Weak transcription	Brain Cingulate Gyrus	brain
15	chr1:154409200-154417600	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr1:154409200-154420600	Weak transcription	Gastric	stomach
17	chr1:154409200-154425800	Weak transcription	Right Atrium	heart
18	chr1:154409400-154424600	Weak transcription	Stomach Mucosa	stomach
19	chr1:154410400-154418000	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
20	chr1:154410800-154418600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
21	chr1:154410800-154418800	Enhancers	Primary T killer memory cells from peripheral blood	blood
22	chr1:154412600-154425800	Weak transcription	Psoas Muscle	Psoas
23	chr1:154412800-154425800	Weak transcription	HepG2	liver
24	chr1:154413000-154419600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr1:154413200-154422600	Weak transcription	Primary B cells from peripheral blood	blood
26	chr1:154413400-154417800	Genic enhancers	Primary mononuclear cells fromperipheralblood	Blood
27	chr1:154413600-154418800	Genic enhancers	Colon Smooth Muscle	Colon
28	chr1:154413600-154419600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr1:154413800-154418800	Genic enhancers	Primary T helper cells fromperipheralblood	blood
30	chr1:154414400-154424400	Strong transcription	Primary monocytes fromperipheralblood	blood
31	chr1:154414400-154424400	Strong transcription	Monocytes-CD14+_RO01746	blood
32	chr1:154414600-154418000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
33	chr1:154414600-154424400	Strong transcription	Primary neutrophils fromperipheralblood	blood
34	chr1:154414600-154426000	Weak transcription	Thymus	Thymus
35	chr1:154414800-154417600	Weak transcription	Primary hematopoietic stem cells	blood
36	chr1:154414800-154417600	Weak transcription	GM12878-XiMat	blood
37	chr1:154414800-154418200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr1:154414800-154418400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr1:154414800-154419000	Genic enhancers	Primary T cells fromperipheralblood	blood
40	chr1:154414800-154436000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
41	chr1:154415000-154417600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr1:154415000-154417600	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
43	chr1:154415000-154417600	Weak transcription	A549	lung
44	chr1:154415000-154418400	Weak transcription	Placenta	Placenta
45	chr1:154415000-154418600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
46	chr1:154415000-154418600	Weak transcription	HSMM	muscle
47	chr1:154415000-154418800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
48	chr1:154415000-154418800	Weak transcription	Placenta Amnion	Placenta Amnion
49	chr1:154415000-154420600	Weak transcription	Pancreas	Pancrea
50	chr1:154415200-154418600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell

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