Variant report

Variant	rs10019240
Chromosome Location	chr4:79583528-79583529
allele	A/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:13)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:13 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr4:79581022..79584954-chr4:79599701..79603406,3	K562	blood:
2	chr4:79581907..79584896-chr4:79611311..79615634,4	K562	blood:
3	chr4:79577188..79580624-chr4:79581809..79584972,3	K562	blood:
4	chr4:79582822..79584593-chr4:79591122..79593119,2	K562	blood:
5	chr4:79582164..79584750-chr4:79606523..79609231,2	MCF-7	breast:
6	chr4:79581815..79583840-chr4:79695430..79698371,3	MCF-7	breast:
7	chr4:79581359..79584183-chr4:79585994..79588670,2	K562	blood:
8	chr4:79581907..79584896-chr4:79611311..79614789,3	K562	blood:
9	chr4:79583221..79584780-chr4:79699632..79701353,2	MCF-7	breast:
10	chr4:79580127..79585145-chr4:79585599..79588670,4	K562	blood:
11	chr4:79573609..79576927-chr4:79583175..79586831,3	MCF-7	breast:
12	chr4:79577940..79580731-chr4:79581809..79584953,3	K562	blood:
13	chr4:79582169..79584322-chr4:79590823..79592622,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000138756	Chromatin interaction
ENSG00000260278	Chromatin interaction

Extended variants
information (count: 69 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs10007186	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10212636	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1107606	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1108907	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11724268	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11724602	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11728013	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11731482	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11733032	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11736376	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11736602	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11942573	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12233694	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12233707	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12643488	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12646646	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12650411	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12711032	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13120630	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13138005	0.82[EUR][1000 genomes]
rs1834518	0.86[EUR][1000 genomes]
rs1972024	0.83[EUR][1000 genomes]
rs28597797	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34325799	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4073678	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4073679	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4074673	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4074674	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4075927	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4077709	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4270605	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4306980	0.83[EUR][1000 genomes]
rs4353930	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4632683	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4643844	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4975148	0.85[EUR][1000 genomes]
rs6533825	0.83[EUR][1000 genomes]
rs6533835	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6533842	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6533845	0.80[AMR][1000 genomes]
rs6811335	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6812227	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6812441	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6814739	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6819484	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6824014	0.83[EUR][1000 genomes]
rs6829061	0.83[EUR][1000 genomes]
rs6829198	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6834587	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6835210	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6835998	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6836513	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6838443	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6840592	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6845893	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6846346	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6851341	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6854055	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7317	0.83[EUR][1000 genomes]
rs7657082	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7669674	0.84[AMR][1000 genomes]
rs7669866	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7670506	0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7680749	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7680766	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7682984	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7689154	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9998136	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1009633	chr4:78887573-79652236	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:86 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:79564400-79589600	Weak transcription	Lung	lung
2	chr4:79573800-79583600	Weak transcription	Colon Smooth Muscle	Colon
3	chr4:79573800-79584200	Weak transcription	Left Ventricle	heart
4	chr4:79573800-79587000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr4:79579400-79588000	Weak transcription	Spleen	Spleen
6	chr4:79579600-79585000	Weak transcription	Placenta	Placenta
7	chr4:79580000-79588000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
8	chr4:79580000-79588000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr4:79580400-79583800	Enhancers	Sigmoid Colon	Sigmoid Colon
10	chr4:79581800-79584400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr4:79581800-79584600	Enhancers	HepG2	liver
12	chr4:79581800-79584800	Enhancers	Brain Cingulate Gyrus	brain
13	chr4:79582000-79588400	Enhancers	Fetal Intestine Large	intestine
14	chr4:79582000-79588600	Enhancers	Fetal Intestine Small	intestine
15	chr4:79582200-79584000	Enhancers	Primary T cells from cord blood	blood
16	chr4:79582400-79583800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr4:79582400-79583800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr4:79582400-79583800	Enhancers	NHLF	lung
19	chr4:79582400-79584000	Enhancers	Stomach Mucosa	stomach
20	chr4:79582400-79584200	Enhancers	Fetal Muscle Leg	muscle
21	chr4:79582400-79584200	Enhancers	Rectal Mucosa Donor 31	rectum
22	chr4:79582400-79584400	Enhancers	Skeletal Muscle Female	skeletal muscle
23	chr4:79582400-79584600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
24	chr4:79582400-79585200	Enhancers	Primary B cells from peripheral blood	blood
25	chr4:79582400-79586600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr4:79582600-79583600	Enhancers	Fetal Lung	lung
27	chr4:79582600-79583600	Enhancers	Small Intestine	intestine
28	chr4:79582600-79583800	Enhancers	Skeletal Muscle Male	skeletal muscle
29	chr4:79582600-79583800	Enhancers	NH-A	brain
30	chr4:79582600-79584400	Enhancers	Adipose Nuclei	Adipose
31	chr4:79582800-79583600	Enhancers	ES-I3 Cell Line	embryonic stem cell
32	chr4:79582800-79583600	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
33	chr4:79582800-79583600	Enhancers	Hela-S3	cervix
34	chr4:79582800-79583800	Enhancers	HUES6 Cell Line	embryonic stem cell
35	chr4:79582800-79583800	Enhancers	iPS-15b Cell Line	embryonic stem cell
36	chr4:79582800-79583800	Enhancers	iPS-20b Cell Line	embryonic stem cell
37	chr4:79582800-79583800	Enhancers	Primary hematopoietic stem cells short term culture	blood
38	chr4:79582800-79583800	Enhancers	Primary T helper cells PMA-I stimulated	--
39	chr4:79582800-79583800	Enhancers	Primary T helper cells fromperipheralblood	blood
40	chr4:79582800-79583800	Enhancers	Cortex derived primary cultured neurospheres	brain
41	chr4:79582800-79583800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr4:79582800-79583800	Enhancers	Liver	Liver
43	chr4:79582800-79584000	Enhancers	Duodenum Smooth Muscle	Duodenum
44	chr4:79582800-79584200	Enhancers	HUES64 Cell Line	embryonic stem cell
45	chr4:79582800-79584200	Enhancers	Primary hematopoietic stem cells	blood
46	chr4:79582800-79584200	Enhancers	Right Atrium	heart
47	chr4:79582800-79584200	Flanking Active TSS	GM12878-XiMat	blood
48	chr4:79582800-79586000	Enhancers	HUES48 Cell Line	embryonic stem cell
49	chr4:79582800-79586800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr4:79583000-79583600	Enhancers	Primary T helper naive cells from peripheral blood	blood

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