Variant report

Variant	rs10516789
Chromosome Location	chr4:88025212-88025213
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:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr4:88016859..88019570-chr4:88023284..88025236,3	MCF-7	breast:
2	chr4:88024363..88026324-chr4:88027975..88030672,2	K562	blood:
3	chr4:88024626..88027340-chr4:88034144..88035743,2	MCF-7	breast:
4	chr4:87945681..87948538-chr4:88025074..88026618,2	MCF-7	breast:
5	chr4:87854450..87858445-chr4:88020078..88026757,11	MCF-7	breast:
6	chr4:87926830..87929105-chr4:88024011..88025624,2	MCF-7	breast:
7	chr4:88013784..88016288-chr4:88023619..88027731,5	MCF-7	breast:
8	chr4:88021442..88026056-chr4:88026505..88030511,4	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000163633	Chromatin interaction
ENSG00000172493	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10018897	0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs168204	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1841265	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs19026	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs236674	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs236675	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs236678	0.95[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs236685	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs236686	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs236687	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2869642	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2926512	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3116679	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs342436	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.80[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs342457	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs342458	0.93[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs342459	0.93[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs342460	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs342461	0.93[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs342462	0.85[CEU][hapmap];0.86[CHB][hapmap];0.92[JPT][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs342465	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AFR][1000 genomes];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3775225	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3822042	0.95[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs384059	0.93[CHB][hapmap];0.92[JPT][hapmap];0.90[ASN][1000 genomes]
rs390604	0.89[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs393991	0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs411365	0.91[ASN][1000 genomes]
rs447990	0.93[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs60757751	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6827213	0.81[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9992235	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[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	chr4:88003400-88028600	Weak transcription	HSMMtube	muscle
4	chr4:88011800-88032800	Weak transcription	Colonic Mucosa	Colon
5	chr4:88015200-88028800	Weak transcription	Aorta	Aorta
6	chr4:88015200-88028800	Weak transcription	Fetal Heart	heart
7	chr4:88015200-88029200	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr4:88015600-88026800	Weak transcription	Fetal Lung	lung
9	chr4:88015800-88035400	Weak transcription	Right Ventricle	heart
10	chr4:88016000-88026400	Weak transcription	Primary B cells from peripheral blood	blood
11	chr4:88016600-88026800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr4:88018000-88026600	Weak transcription	Cortex derived primary cultured neurospheres	brain
13	chr4:88018600-88029200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr4:88018600-88034200	Weak transcription	Fetal Stomach	stomach
15	chr4:88019000-88072200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr4:88020200-88025400	Weak transcription	Pancreatic Islets	Pancreatic Islet
17	chr4:88021000-88029200	Weak transcription	Ovary	ovary
18	chr4:88021000-88034200	Weak transcription	Spleen	Spleen
19	chr4:88021200-88029200	Weak transcription	Brain Hippocampus Middle	brain
20	chr4:88021400-88026400	Weak transcription	Brain Substantia Nigra	brain
21	chr4:88021600-88026400	Weak transcription	H1 Cell Line	embryonic stem cell
22	chr4:88021600-88026400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr4:88021600-88026800	Weak transcription	Fetal Thymus	thymus
24	chr4:88021600-88028800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr4:88021600-88029200	Weak transcription	Right Atrium	heart
26	chr4:88021600-88036600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr4:88021600-88037800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr4:88021800-88029000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr4:88021800-88029200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr4:88021800-88029400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr4:88021800-88036000	Weak transcription	Brain Angular Gyrus	brain
32	chr4:88022000-88026600	Weak transcription	HUES64 Cell Line	embryonic stem cell
33	chr4:88022200-88026800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
34	chr4:88022400-88026600	Weak transcription	HUES6 Cell Line	embryonic stem cell
35	chr4:88022400-88027400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
36	chr4:88022600-88027000	Enhancers	Primary T helper cells PMA-I stimulated	--
37	chr4:88022800-88025800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr4:88022800-88026800	Weak transcription	Thymus	Thymus
39	chr4:88022800-88027200	Enhancers	NHEK	skin
40	chr4:88023000-88026400	Weak transcription	HUES48 Cell Line	embryonic stem cell
41	chr4:88023000-88028600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
42	chr4:88023200-88026200	Weak transcription	Monocytes-CD14+_RO01746	blood
43	chr4:88023200-88026400	Enhancers	Primary T cells from cord blood	blood
44	chr4:88023200-88026600	Weak transcription	Primary monocytes fromperipheralblood	blood
45	chr4:88023200-88026600	Weak transcription	Primary neutrophils fromperipheralblood	blood
46	chr4:88023200-88027000	Enhancers	Colon Smooth Muscle	Colon
47	chr4:88023400-88026400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
48	chr4:88023400-88027000	Enhancers	Breast Myoepithelial Primary Cells	Breast
49	chr4:88023400-88027000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
50	chr4:88023400-88027000	Enhancers	Primary T helper naive cells fromperipheralblood	blood

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