Variant report

Variant	rs55787557
Chromosome Location	chr4:87950825-87950826
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:87944178..87948145-chr4:87950244..87953545,6	K562	blood:
2	chr4:87924739..87931529-chr4:87944789..87955863,16	K562	blood:
3	chr4:87944954..87950016-chr4:87950159..87955839,10	K562	blood:
4	chr4:87950378..87952064-chr4:87953827..87955577,2	MCF-7	breast:
5	chr4:87926723..87929502-chr4:87950750..87952637,2	MCF-7	breast:
6	chr4:87934960..87936958-chr4:87949259..87951055,2	MCF-7	breast:
7	chr20:46131389..46132897-chr4:87950078..87952930,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000172493	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10516788	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1471251	0.95[ASN][1000 genomes]
rs17012200	0.81[ASN][1000 genomes]
rs17012213	0.81[ASN][1000 genomes]
rs17012234	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17604480	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17701999	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17752307	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2061498	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs4693801	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs55816619	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs55879154	0.87[AFR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs55913164	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs55982755	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs56023922	0.85[ASN][1000 genomes]
rs56050898	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56201818	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56378441	0.81[ASN][1000 genomes]
rs56390363	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56395939	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56406125	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6819155	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6840258	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6854749	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72667735	0.81[ASN][1000 genomes]
rs72667736	0.81[ASN][1000 genomes]
rs72667737	0.81[ASN][1000 genomes]
rs72667739	0.81[ASN][1000 genomes]
rs72667747	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72667748	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72667750	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72667751	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72667752	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72667753	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72667754	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72667757	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72667759	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72667765	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7665282	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs767315	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7682652	0.87[AFR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7695426	0.90[AFR][1000 genomes];0.86[EUR][1000 genomes];0.90[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	nsv1009937	chr4:87795314-88008345	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases
2	nsv999176	chr4:87869996-88098136	Strong transcription Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
3	nsv998335	chr4:87869996-88104414	Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	nsv1001017	chr4:87872160-88087003	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
5	nsv537166	chr4:87872160-88087003	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
6	nsv999098	chr4:87899091-88016048	Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
7	nsv537167	chr4:87899091-88016048	Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
8	nsv997750	chr4:87933945-88264127	Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:87935800-87951000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
2	chr4:87937000-87951800	Weak transcription	NHEK	skin
3	chr4:87937000-87952000	Weak transcription	HMEC	breast
4	chr4:87943200-87951400	Weak transcription	Fetal Brain Male	brain
5	chr4:87944200-87951800	Enhancers	Skeletal Muscle Male	skeletal muscle
6	chr4:87944200-87951800	Enhancers	K562	blood
7	chr4:87944200-87953000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr4:87944200-87960800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr4:87944800-87961600	Enhancers	Fetal Heart	heart
10	chr4:87945000-87951800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr4:87945400-87951200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr4:87945600-87952000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr4:87946400-87951000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr4:87946600-87951600	Weak transcription	Muscle Satellite Cultured Cells	--
15	chr4:87946600-87951600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr4:87946600-87952000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
17	chr4:87947000-87952000	Enhancers	Rectal Smooth Muscle	rectum
18	chr4:87947200-87952000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr4:87947200-87952000	Weak transcription	Gastric	stomach
20	chr4:87947800-87951000	Weak transcription	Primary T helper cells fromperipheralblood	blood
21	chr4:87947800-87951400	Weak transcription	H1 Cell Line	embryonic stem cell
22	chr4:87947800-87951400	Weak transcription	H9 Cell Line	embryonic stem cell
23	chr4:87947800-87951800	Weak transcription	Primary T cells fromperipheralblood	blood
24	chr4:87947800-87951800	Enhancers	Colon Smooth Muscle	Colon
25	chr4:87947800-87951800	Weak transcription	Esophagus	oesophagus
26	chr4:87947800-87952000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr4:87947800-87952000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
28	chr4:87947800-87952000	Weak transcription	Lung	lung
29	chr4:87947800-87957200	Weak transcription	Dnd41	blood
30	chr4:87948000-87951800	Weak transcription	HepG2	liver
31	chr4:87948000-87954200	Weak transcription	A549	lung
32	chr4:87948400-87951000	Weak transcription	Brain Cingulate Gyrus	brain
33	chr4:87948400-87951800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
34	chr4:87948600-87951000	Weak transcription	Pancreatic Islets	Pancreatic Islet
35	chr4:87948600-87951400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
36	chr4:87948600-87951800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr4:87948600-87951800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
38	chr4:87948600-87951800	Weak transcription	Brain Inferior Temporal Lobe	brain
39	chr4:87948800-87951000	Enhancers	Primary B cells from cord blood	blood
40	chr4:87948800-87952000	Weak transcription	Rectal Mucosa Donor 29	rectum
41	chr4:87949200-87951000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr4:87949200-87951000	Enhancers	Stomach Mucosa	stomach
43	chr4:87949200-87951800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
44	chr4:87949200-87952000	Enhancers	iPS-15b Cell Line	embryonic stem cell
45	chr4:87949200-87952000	Weak transcription	Primary B cells from peripheral blood	blood
46	chr4:87949200-87957400	Weak transcription	Monocytes-CD14+_RO01746	blood
47	chr4:87949200-87961000	Enhancers	HUES64 Cell Line	embryonic stem cell
48	chr4:87949400-87960600	Enhancers	Liver	Liver
49	chr4:87949600-87954000	Enhancers	Primary T helper naive cells from peripheral blood	blood
50	chr4:87949600-87955600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood

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