Variant report

Variant	rs56406125
Chromosome Location	chr4:87940205-87940206
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:87938501..87940925-chr4:87946524..87948135,2	K562	blood:
2	chr4:87938807..87941655-chr4:87943072..87944997,3	K562	blood:
3	chr4:87854648..87860283-chr4:87935219..87941983,10	K562	blood:
4	chr4:87926199..87928138-chr4:87938575..87940535,2	MCF-7	breast:
5	chr4:87938324..87940317-chr4:87979217..87981960,2	K562	blood:
6	chr4:87938104..87941655-chr4:87942635..87944997,3	K562	blood:
7	chr4:87853595..87871697-chr4:87924007..87941983,77	K562	blood:

Variant related genes	Relation type
ENSG00000172493	Chromatin interaction
ENSG00000235043	Chromatin interaction
ENSG00000163633	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10516785	0.84[ASN][1000 genomes]
rs10516786	0.84[ASN][1000 genomes]
rs10516788	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1471251	0.87[ASN][1000 genomes]
rs17012200	0.86[ASN][1000 genomes]
rs17012213	0.86[ASN][1000 genomes]
rs17012216	0.84[ASN][1000 genomes]
rs17012234	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17604480	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17701999	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17752307	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4693795	0.82[ASN][1000 genomes]
rs4693801	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55787557	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs55816619	0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs55851914	0.84[ASN][1000 genomes]
rs55879154	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs55913164	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs56023922	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56050898	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56201818	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs56378441	0.86[ASN][1000 genomes]
rs56390363	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56395939	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6819155	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6840258	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6854749	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72667735	0.86[ASN][1000 genomes]
rs72667736	0.86[ASN][1000 genomes]
rs72667737	0.86[ASN][1000 genomes]
rs72667739	0.86[ASN][1000 genomes]
rs72667741	0.83[ASN][1000 genomes]
rs72667747	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72667748	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72667750	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72667751	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72667752	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72667753	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72667754	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72667757	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72667759	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72667765	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7665282	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs767315	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7682652	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7695426	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[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:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:87929400-87946200	Weak transcription	Esophagus	oesophagus
2	chr4:87930600-87940600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
3	chr4:87930600-87946800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr4:87930600-87950000	Weak transcription	Fetal Stomach	stomach
5	chr4:87930800-87940600	Weak transcription	Spleen	Spleen
6	chr4:87931000-87940800	Enhancers	Primary neutrophils fromperipheralblood	blood
7	chr4:87931000-87940800	Enhancers	Rectal Mucosa Donor 31	rectum
8	chr4:87931000-87946600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr4:87931200-87940400	Enhancers	Primary B cells from cord blood	blood
10	chr4:87931200-87943400	Enhancers	Primary T helper cells PMA-I stimulated	--
11	chr4:87931800-87942600	Enhancers	Primary hematopoietic stem cells	blood
12	chr4:87933200-87941000	Enhancers	HUES64 Cell Line	embryonic stem cell
13	chr4:87934400-87940800	Enhancers	Fetal Intestine Small	intestine
14	chr4:87935200-87940400	Enhancers	Liver	Liver
15	chr4:87935400-87942000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr4:87935600-87941000	Enhancers	HUES6 Cell Line	embryonic stem cell
17	chr4:87935600-87950200	Weak transcription	Fetal Muscle Leg	muscle
18	chr4:87935800-87941600	Enhancers	Dnd41	blood
19	chr4:87935800-87945000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
20	chr4:87935800-87951000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
21	chr4:87936000-87942600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr4:87936000-87950000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr4:87936400-87941600	Enhancers	Primary hematopoietic stem cells short term culture	blood
24	chr4:87936400-87945000	Weak transcription	Cortex derived primary cultured neurospheres	brain
25	chr4:87937000-87946200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
26	chr4:87937000-87950400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr4:87937000-87951800	Weak transcription	NHEK	skin
28	chr4:87937000-87952000	Weak transcription	HMEC	breast
29	chr4:87937400-87940400	Weak transcription	Duodenum Mucosa	Duodenum
30	chr4:87937400-87946200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr4:87937600-87941400	Enhancers	iPS-15b Cell Line	embryonic stem cell
32	chr4:87937600-87949800	Weak transcription	Placenta Amnion	Placenta Amnion
33	chr4:87937800-87940800	Enhancers	Monocytes-CD14+_RO01746	blood
34	chr4:87938000-87941000	Enhancers	HUES48 Cell Line	embryonic stem cell
35	chr4:87938000-87941200	Enhancers	Fetal Heart	heart
36	chr4:87938000-87942600	Enhancers	Primary T killer memory cells from peripheral blood	blood
37	chr4:87938000-87944800	Weak transcription	Rectal Mucosa Donor 29	rectum
38	chr4:87938200-87941400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr4:87938600-87941000	Enhancers	Placenta	Placenta
40	chr4:87938600-87942400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr4:87938600-87943000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
42	chr4:87938800-87940600	Enhancers	Brain Anterior Caudate	brain
43	chr4:87938800-87940800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr4:87938800-87940800	Enhancers	Ovary	ovary
45	chr4:87938800-87940800	Enhancers	Psoas Muscle	Psoas
46	chr4:87938800-87940800	Enhancers	Stomach Mucosa	stomach
47	chr4:87938800-87941000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
48	chr4:87938800-87941000	Enhancers	Right Atrium	heart
49	chr4:87938800-87941000	Enhancers	Sigmoid Colon	Sigmoid Colon
50	chr4:87938800-87941000	Enhancers	Skeletal Muscle Female	skeletal muscle

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