Variant report

Variant	rs11742668
Chromosome Location	chr5:79939904-79939905
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:79939684..79942536-chr5:79944291..79945964,2	MCF-7	breast:

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10036264	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10052238	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10054574	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10057770	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10072026	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.89[EUR][1000 genomes]
rs10077031	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10078190	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10213944	0.85[EUR][1000 genomes]
rs10474631	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10474632	1.00[CEU][hapmap];0.81[TSI][hapmap];0.87[EUR][1000 genomes]
rs10474634	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11741448	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11742720	0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11749051	0.91[EUR][1000 genomes]
rs13355622	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3797888	0.84[YRI][hapmap]
rs56270084	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6151599	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6151606	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6151640	1.00[CEU][hapmap];1.00[GIH][hapmap];0.95[TSI][hapmap];0.90[EUR][1000 genomes]
rs6151655	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6151725	0.84[AFR][1000 genomes]
rs6151735	0.84[AFR][1000 genomes]
rs6453522	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs67695365	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs72765574	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72765575	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[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	nsv1024844	chr5:79862428-80860430	Weak transcription Strong transcription Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:79906600-79949200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr5:79912200-79948000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
3	chr5:79913200-79949000	Weak transcription	Spleen	Spleen
4	chr5:79913600-79949400	Weak transcription	Esophagus	oesophagus
5	chr5:79914200-79949400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr5:79915400-79949200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr5:79916600-79949400	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr5:79919600-79949200	Weak transcription	Colonic Mucosa	Colon
9	chr5:79919600-79949800	Weak transcription	Pancreas	Pancrea
10	chr5:79919800-79949000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr5:79920200-79949000	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr5:79920200-79949000	Weak transcription	Stomach Mucosa	stomach
13	chr5:79923600-79949800	Weak transcription	Brain Hippocampus Middle	brain
14	chr5:79924200-79949200	Weak transcription	Colon Smooth Muscle	Colon
15	chr5:79924200-79949400	Weak transcription	Right Ventricle	heart
16	chr5:79924200-79949800	Weak transcription	Left Ventricle	heart
17	chr5:79924400-79945800	Strong transcription	Dnd41	blood
18	chr5:79924400-79949200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr5:79924600-79940000	Weak transcription	Fetal Heart	heart
20	chr5:79924800-79943000	Weak transcription	Brain Germinal Matrix	brain
21	chr5:79925000-79946200	Strong transcription	HUES64 Cell Line	embryonic stem cell
22	chr5:79925200-79945600	Strong transcription	Fetal Thymus	thymus
23	chr5:79925200-79945800	Strong transcription	HUES6 Cell Line	embryonic stem cell
24	chr5:79925200-79948400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
25	chr5:79925200-79948600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
26	chr5:79925600-79949600	Weak transcription	HSMMtube	muscle
27	chr5:79926000-79942000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr5:79926800-79945000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr5:79926800-79945800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr5:79927200-79945000	Strong transcription	HMEC	breast
31	chr5:79927200-79945400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
32	chr5:79927200-79945800	Strong transcription	HUES48 Cell Line	embryonic stem cell
33	chr5:79928000-79944200	Weak transcription	Aorta	Aorta
34	chr5:79928600-79949200	Weak transcription	NH-A	brain
35	chr5:79929000-79949800	Weak transcription	Brain Inferior Temporal Lobe	brain
36	chr5:79929200-79949200	Weak transcription	Fetal Brain Male	brain
37	chr5:79929400-79949400	Weak transcription	Rectal Smooth Muscle	rectum
38	chr5:79930000-79945000	Strong transcription	Cortex derived primary cultured neurospheres	brain
39	chr5:79930400-79945000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr5:79930600-79944800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr5:79930800-79945600	Strong transcription	Liver	Liver
42	chr5:79931400-79949200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
43	chr5:79931600-79945000	Strong transcription	Primary T helper cells fromperipheralblood	blood
44	chr5:79931800-79944600	Strong transcription	Fetal Muscle Leg	muscle
45	chr5:79932000-79941200	Strong transcription	Monocytes-CD14+_RO01746	blood
46	chr5:79932000-79945800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
47	chr5:79932400-79946400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
48	chr5:79932600-79941800	Strong transcription	Primary monocytes fromperipheralblood	blood
49	chr5:79932600-79944800	Strong transcription	A549	lung
50	chr5:79932800-79945600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links