Variant report

Variant	rs3755985
Chromosome Location	chr4:88024738-88024739
allele	C/T
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:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr4:88016859..88019570-chr4:88023284..88025236,3	MCF-7	breast:
2	chr4:88023345..88024906-chr4:88040563..88042654,2	MCF-7	breast:
3	chr4:88023177..88025115-chr4:88372900..88374503,2	K562	blood:
4	chr4:88024363..88026324-chr4:88027975..88030672,2	K562	blood:
5	chr4:88024626..88027340-chr4:88034144..88035743,2	MCF-7	breast:
6	chr4:87854450..87858445-chr4:88020078..88026757,11	MCF-7	breast:
7	chr4:87926830..87929105-chr4:88024011..88025624,2	MCF-7	breast:
8	chr4:88022117..88024925-chr4:88027985..88030710,2	K562	blood:
9	chr4:88013784..88016288-chr4:88023619..88027731,5	MCF-7	breast:
10	chr4:88021442..88026056-chr4:88026505..88030511,4	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000172493	Chromatin interaction
ENSG00000163633	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10018904	0.86[ASN][1000 genomes]
rs10023056	0.90[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10029915	0.85[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10032710	0.90[CEU][hapmap];0.90[CHB][hapmap];0.89[JPT][hapmap];0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13120301	0.86[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs151450	0.97[ASN][1000 genomes]
rs151451	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17012334	0.81[CEU][hapmap];0.87[EUR][1000 genomes]
rs17012512	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17605615	1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs17668131	0.86[ASN][1000 genomes]
rs1842685	0.90[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2035403	0.99[ASN][1000 genomes]
rs2061498	0.88[EUR][1000 genomes]
rs2280952	0.86[ASN][1000 genomes]
rs2280954	0.94[JPT][hapmap];0.86[ASN][1000 genomes]
rs236676	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs236679	0.86[ASN][1000 genomes]
rs236681	0.85[CHB][hapmap];0.94[JPT][hapmap];0.85[ASN][1000 genomes]
rs3733377	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3736668	0.95[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3755980	0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3755983	1.00[CHB][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3775209	0.89[JPT][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3775211	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3775226	0.85[CEU][hapmap];0.85[CHB][hapmap];0.94[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3775228	0.85[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs55747890	0.86[AFR][1000 genomes]
rs55982755	0.88[EUR][1000 genomes]
rs56023922	1.00[AFR][1000 genomes]
rs60695258	0.99[ASN][1000 genomes]
rs66477840	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	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
6	nsv879525	chr4:87964363-88033352	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:87995200-88029200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr4:87995400-88037800	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr4:88001400-88025200	Weak transcription	Fetal Muscle Leg	muscle
4	chr4:88001800-88025200	Weak transcription	Gastric	stomach
5	chr4:88003400-88028600	Weak transcription	HSMMtube	muscle
6	chr4:88004400-88025200	Weak transcription	Fetal Muscle Trunk	muscle
7	chr4:88011800-88032800	Weak transcription	Colonic Mucosa	Colon
8	chr4:88014800-88024800	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr4:88015200-88025200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr4:88015200-88025200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr4:88015200-88028800	Weak transcription	Aorta	Aorta
12	chr4:88015200-88028800	Weak transcription	Fetal Heart	heart
13	chr4:88015200-88029200	Weak transcription	Brain Inferior Temporal Lobe	brain
14	chr4:88015400-88025200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr4:88015400-88025200	Weak transcription	Esophagus	oesophagus
16	chr4:88015400-88025200	Weak transcription	Left Ventricle	heart
17	chr4:88015400-88025200	Weak transcription	Skeletal Muscle Male	skeletal muscle
18	chr4:88015600-88026800	Weak transcription	Fetal Lung	lung
19	chr4:88015800-88024800	Weak transcription	HMEC	breast
20	chr4:88015800-88035400	Weak transcription	Right Ventricle	heart
21	chr4:88016000-88026400	Weak transcription	Primary B cells from peripheral blood	blood
22	chr4:88016600-88026800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
23	chr4:88018000-88026600	Weak transcription	Cortex derived primary cultured neurospheres	brain
24	chr4:88018200-88025200	Weak transcription	Primary T cells fromperipheralblood	blood
25	chr4:88018600-88024800	Weak transcription	Rectal Mucosa Donor 29	rectum
26	chr4:88018600-88024800	Weak transcription	Skeletal Muscle Female	skeletal muscle
27	chr4:88018600-88025200	Weak transcription	Lung	lung
28	chr4:88018600-88025200	Weak transcription	Stomach Smooth Muscle	stomach
29	chr4:88018600-88029200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr4:88018600-88034200	Weak transcription	Fetal Stomach	stomach
31	chr4:88019000-88072200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
32	chr4:88020200-88025400	Weak transcription	Pancreatic Islets	Pancreatic Islet
33	chr4:88021000-88029200	Weak transcription	Ovary	ovary
34	chr4:88021000-88034200	Weak transcription	Spleen	Spleen
35	chr4:88021200-88029200	Weak transcription	Brain Hippocampus Middle	brain
36	chr4:88021400-88026400	Weak transcription	Brain Substantia Nigra	brain
37	chr4:88021600-88025200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
38	chr4:88021600-88025200	Weak transcription	Pancreas	Pancrea
39	chr4:88021600-88026400	Weak transcription	H1 Cell Line	embryonic stem cell
40	chr4:88021600-88026400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr4:88021600-88026800	Weak transcription	Fetal Thymus	thymus
42	chr4:88021600-88028800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr4:88021600-88029200	Weak transcription	Right Atrium	heart
44	chr4:88021600-88036600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr4:88021600-88037800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
46	chr4:88021800-88025000	Weak transcription	Small Intestine	intestine
47	chr4:88021800-88029000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
48	chr4:88021800-88029200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr4:88021800-88029400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr4:88021800-88036000	Weak transcription	Brain Angular Gyrus	brain

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