Variant report

Variant	rs1060419
Chromosome Location	chr6:79944994-79944995
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:6)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:4)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:6 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	KAP1	chr6:79943222-79945113	HEK293	kidney:	n/a	chr6:79943761-79943769
2	EP300	chr6:79944918-79945118	GM12878	blood:	n/a	n/a
3	POLR2A	chr6:79942900-79945349	MCF10A-Er-Src	breast:	n/a	n/a
4	RFX5	chr6:79942075-79945226	SK-N-SH	brain:	n/a	chr6:79944581-79944596
5	KAP1	chr6:79942796-79945275	U2OS	brain:	n/a	chr6:79943761-79943769
6	E2F4	chr6:79944167-79945004	GM12878	blood:	n/a	n/a

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:79785425..79789135-chr6:79942833..79950296,12	MCF-7	breast:
2	chr6:79782683..79789958-chr6:79939846..79945776,22	MCF-7	breast:
3	chr6:79787878..79790499-chr6:79943656..79946271,3	K562	blood:
4	chr6:79785468..79790645-chr6:79941426..79946271,8	K562	blood:

(count:4 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-IRAK1BP1-1	chr6:79943779-79946510	ENSG00000247783
2	lnc-IRAK1BP1-1	chr6:79943779-79946517	NONHSAT113679
3	lnc-IRAK1BP1-1	chr6:79944457-79946310	NONHSAT113680
4	lnc-IRAK1BP1-1	chr6:79943779-79946514	ENSG00000270362.1

No data

Variant related genes	Relation type
HMGN3	TF binding region
ENSG00000146247	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs11759494	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.86[TSI][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12191682	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs1335539	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];0.83[MEX][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2065752	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2322217	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2322218	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4112503	0.94[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs4272177	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4499887	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];0.83[MEX][hapmap];0.93[TSI][hapmap];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6931935	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7742739	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7757529	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]

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	nsv830706	chr6:79825910-79994878	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv1028607	chr6:79853272-80767716	Enhancers Active TSS Genic enhancers Flanking Active TSS Strong transcription Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:79941600-79945000	Active TSS	iPS-20b Cell Line	embryonic stem cell
2	chr6:79942800-79945000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr6:79942800-79945000	Active TSS	A549	lung
4	chr6:79943000-79945000	Active TSS	ES-I3 Cell Line	embryonic stem cell
5	chr6:79943000-79945000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr6:79943000-79945000	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr6:79943000-79945000	Active TSS	HUES64 Cell Line	embryonic stem cell
8	chr6:79943000-79945000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr6:79943000-79945000	Active TSS	Adipose Nuclei	Adipose
10	chr6:79943000-79945000	Active TSS	Brain Hippocampus Middle	brain
11	chr6:79943000-79945000	Active TSS	Brain Inferior Temporal Lobe	brain
12	chr6:79943000-79945000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
13	chr6:79943000-79945000	Active TSS	Brain Substantia Nigra	brain
14	chr6:79943000-79945000	Active TSS	Fetal Kidney	kidney
15	chr6:79943000-79945000	Active TSS	Fetal Lung	lung
16	chr6:79943000-79945000	Active TSS	Psoas Muscle	Psoas
17	chr6:79943000-79945000	Active TSS	Stomach Smooth Muscle	stomach
18	chr6:79943000-79945000	Active TSS	K562	blood
19	chr6:79943200-79945000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr6:79943200-79945000	Active TSS	Aorta	Aorta
21	chr6:79943200-79945000	Active TSS	Rectal Smooth Muscle	rectum
22	chr6:79943400-79945000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr6:79944400-79945000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
24	chr6:79944400-79945000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
25	chr6:79944400-79945000	Flanking Active TSS	Fetal Thymus	thymus
26	chr6:79944400-79948400	Weak transcription	Left Ventricle	heart
27	chr6:79944400-79948600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr6:79944400-79948600	Weak transcription	Stomach Mucosa	stomach
29	chr6:79944400-79948800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
30	chr6:79944400-79950400	Weak transcription	Lung	lung
31	chr6:79944600-79945000	Enhancers	Primary monocytes fromperipheralblood	blood
32	chr6:79944600-79945000	Enhancers	Primary B cells from peripheral blood	blood
33	chr6:79944600-79945000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
34	chr6:79944600-79945000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr6:79944600-79945000	Flanking Active TSS	Dnd41	blood
36	chr6:79944600-79948600	Weak transcription	Ovary	ovary
37	chr6:79944600-79948600	Weak transcription	Pancreas	Pancrea
38	chr6:79944600-79948600	Weak transcription	Sigmoid Colon	Sigmoid Colon
39	chr6:79944800-79945000	Active TSS	HUES6 Cell Line	embryonic stem cell
40	chr6:79944800-79945000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr6:79944800-79945000	Enhancers	Primary T cells fromperipheralblood	blood
42	chr6:79944800-79945000	Enhancers	Primary T helper cells PMA-I stimulated	--
43	chr6:79944800-79945000	Enhancers	Primary T helper cells fromperipheralblood	blood
44	chr6:79944800-79945000	Enhancers	Primary T killer memory cells from peripheral blood	blood
45	chr6:79944800-79945000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr6:79944800-79945000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr6:79944800-79945000	Enhancers	Colon Smooth Muscle	Colon
48	chr6:79944800-79945000	Enhancers	Fetal Heart	heart
49	chr6:79944800-79945000	Enhancers	Pancreatic Islets	Pancreatic Islet
50	chr6:79944800-79945000	Enhancers	Placenta	Placenta

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