Variant report

Variant	rs4689560
Chromosome Location	chr4:6928570-6928571
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:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr4:6926884..6928623-chr4:6939746..6942582,2	MCF-7	breast:
2	chr4:6917201..6921579-chr4:6924492..6930074,6	MCF-7	breast:
3	chr4:6909963..6912664-chr4:6925024..6930247,5	MCF-7	breast:
4	chr4:6926678..6929634-chr4:6988002..6989801,2	K562	blood:
5	chr4:6927493..6929739-chr4:6946981..6949624,2	K562	blood:
6	chr4:6928082..6930342-chr4:6930567..6933330,2	MCF-7	breast:
7	chr4:6927079..6929497-chr4:6940863..6942665,2	K562	blood:
8	chr4:6927466..6930094-chr4:7020098..7022400,2	MCF-7	breast:
9	chr4:6926678..6930436-chr4:6987384..6989801,3	K562	blood:
10	chr4:6925139..6926793-chr4:6927424..6929653,2	K562	blood:
11	chr4:6927079..6929042-chr4:6940771..6942363,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000132405	Chromatin interaction

Extended variants
information (count: 62 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs10012590	0.83[CEU][hapmap];1.00[CHB][hapmap]
rs10937774	1.00[CHB][hapmap]
rs11732898	1.00[CHB][hapmap]
rs11938701	0.81[AMR][1000 genomes]
rs12503027	0.81[AMR][1000 genomes]
rs12512484	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13108082	0.83[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs13111887	0.80[ASN][1000 genomes]
rs13115245	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13115617	1.00[CHB][hapmap]
rs13122119	1.00[CHB][hapmap];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13141777	0.82[AMR][1000 genomes]
rs13144485	0.86[AMR][1000 genomes]
rs13148395	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13149411	0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13149923	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2301817	1.00[CHB][hapmap]
rs2301818	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2301819	0.86[ASN][1000 genomes]
rs3188939	0.83[CEU][hapmap];1.00[CHB][hapmap]
rs34221933	0.90[EUR][1000 genomes]
rs34335938	0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34379427	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34463709	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34481892	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34860182	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34953654	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs34959511	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34990775	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35170004	0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs35680216	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3892490	1.00[CHB][hapmap]
rs3894945	0.81[AMR][1000 genomes]
rs4234788	0.80[ASN][1000 genomes]
rs4234791	1.00[CHB][hapmap];0.86[ASN][1000 genomes]
rs4544710	0.83[CEU][hapmap];1.00[CHB][hapmap];0.84[EUR][1000 genomes]
rs4689056	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4689563	0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs4689564	0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs4689565	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4689568	1.00[CHB][hapmap]
rs4689575	0.81[CEU][hapmap];1.00[CHB][hapmap]
rs62289166	0.84[AMR][1000 genomes]
rs6446559	0.80[ASN][1000 genomes]
rs66530709	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs66640699	0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs66841627	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs66931928	0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs66992702	0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs6811496	0.81[AMR][1000 genomes]
rs6816660	0.80[ASN][1000 genomes]
rs6818744	0.83[CEU][hapmap];1.00[CHB][hapmap];0.81[AMR][1000 genomes]
rs6840780	0.89[EUR][1000 genomes]
rs6854776	0.83[CEU][hapmap];1.00[CHB][hapmap]
rs7655563	1.00[CHB][hapmap]
rs7655773	0.90[CEU][hapmap];1.00[CHB][hapmap];0.90[EUR][1000 genomes]
rs7658198	1.00[CHB][hapmap]
rs7661462	1.00[CHB][hapmap]
rs7661952	0.83[CEU][hapmap];1.00[CHB][hapmap];0.84[EUR][1000 genomes]
rs7675524	1.00[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv878529	chr4:6883012-6983677	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
2	nsv878530	chr4:6888932-7058473	Strong transcription Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 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	chr4:6919600-6942200	Weak transcription	Hela-S3	cervix
2	chr4:6920200-6939600	Weak transcription	HUVEC	blood vessel
3	chr4:6920400-6928600	Weak transcription	Psoas Muscle	Psoas
4	chr4:6920400-6931000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr4:6923200-6930800	Weak transcription	Stomach Mucosa	stomach
6	chr4:6924400-6930600	Weak transcription	Fetal Brain Male	brain
7	chr4:6924600-6928600	Weak transcription	Osteobl	bone
8	chr4:6924600-6929000	Strong transcription	Fetal Stomach	stomach
9	chr4:6925000-6928800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr4:6925400-6928800	Genic enhancers	Spleen	Spleen
11	chr4:6925800-6931400	Weak transcription	HSMMtube	muscle
12	chr4:6926000-6928600	Weak transcription	A549	lung
13	chr4:6926000-6930600	Weak transcription	Pancreatic Islets	Pancreatic Islet
14	chr4:6926200-6930800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr4:6926200-6942000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
16	chr4:6926200-6942600	Weak transcription	NHEK	skin
17	chr4:6926200-6943200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr4:6926400-6928600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr4:6926400-6928600	Weak transcription	NHLF	lung
20	chr4:6926600-6928600	Weak transcription	HUES6 Cell Line	embryonic stem cell
21	chr4:6926600-6928600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr4:6926600-6928600	Weak transcription	Left Ventricle	heart
23	chr4:6926600-6928800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr4:6926600-6929600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
25	chr4:6926600-6930800	Weak transcription	Brain Angular Gyrus	brain
26	chr4:6926600-6930800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
27	chr4:6926600-6931000	Weak transcription	HUES48 Cell Line	embryonic stem cell
28	chr4:6926600-6932200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
29	chr4:6926600-6933400	Enhancers	Primary monocytes fromperipheralblood	blood
30	chr4:6926600-6935000	Enhancers	Liver	Liver
31	chr4:6926600-6939200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
32	chr4:6926800-6929600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr4:6926800-6930600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
34	chr4:6926800-6932200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
35	chr4:6927000-6928600	Enhancers	Primary T helper naive cells from peripheral blood	blood
36	chr4:6927000-6928600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
37	chr4:6927000-6928600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr4:6927000-6928600	Weak transcription	Ovary	ovary
39	chr4:6927000-6929200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
40	chr4:6927000-6930600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr4:6927200-6928800	Genic enhancers	GM12878-XiMat	blood
42	chr4:6927200-6929000	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells short term culture	blood
43	chr4:6927200-6932200	Enhancers	Adipose Nuclei	Adipose
44	chr4:6927200-6932200	Genic enhancers	Thymus	Thymus
45	chr4:6927400-6928600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
46	chr4:6927400-6929400	Weak transcription	Brain Germinal Matrix	brain
47	chr4:6927400-6929600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
48	chr4:6927400-6930400	Weak transcription	Cortex derived primary cultured neurospheres	brain
49	chr4:6927600-6928600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
50	chr4:6927600-6928600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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