Variant report

Variant	rs1859109
Chromosome Location	chr7:27956078-27956079
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	chr7:27956076..27958841-chr7:27959567..27962104,2	MCF-7	breast:

Extended variants
information (count: 39 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10249314	0.82[CEU][hapmap]
rs10951187	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11763181	1.00[CEU][hapmap]
rs12538288	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1557779	0.85[CEU][hapmap]
rs191	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs197	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs200	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs201	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs205	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs207	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs208	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2097737	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs211	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs213	1.00[CEU][hapmap]
rs214	1.00[AFR][1000 genomes]
rs215	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs218	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4722746	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6462060	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6951040	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6955462	0.82[CEU][hapmap]
rs6958293	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6968362	1.00[CEU][hapmap]
rs6968677	1.00[CEU][hapmap]
rs6969949	1.00[CEU][hapmap]
rs6970113	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6972944	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73083394	0.91[EUR][1000 genomes]
rs7778340	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7783410	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7787507	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs916854	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][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	nsv949025	chr7:27578167-28075172	Active TSS Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
2	esv2758109	chr7:27793616-27972869	Weak transcription Genic enhancers Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
3	esv2759520	chr7:27793616-27972869	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
4	nsv1030685	chr7:27844038-28177301	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
5	nsv1024819	chr7:27949955-28020969	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer	Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv520555	chr7:27952629-27958750	Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:27937600-27956200	Weak transcription	Gastric	stomach
2	chr7:27941200-27956200	Weak transcription	Aorta	Aorta
3	chr7:27941400-27957600	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr7:27941400-27990800	Weak transcription	Primary T cells from cord blood	blood
5	chr7:27941600-27962800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr7:27942400-28005600	Weak transcription	Primary monocytes fromperipheralblood	blood
7	chr7:27949000-27957400	Weak transcription	Primary B cells from peripheral blood	blood
8	chr7:27950400-27957400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr7:27950400-27963000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr7:27950600-27956800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr7:27950600-27957000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr7:27950600-27957000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr7:27950600-27957200	Weak transcription	HSMMtube	muscle
14	chr7:27950800-27958200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr7:27951400-27963000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr7:27952600-27959000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr7:27952600-27960200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr7:27953600-27959400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
19	chr7:27954000-27957000	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr7:27954200-27959600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
21	chr7:27954400-27956800	Weak transcription	Rectal Smooth Muscle	rectum
22	chr7:27954400-27959600	Weak transcription	H1 Cell Line	embryonic stem cell
23	chr7:27954600-27957000	Weak transcription	Fetal Heart	heart
24	chr7:27954600-27957200	Weak transcription	Muscle Satellite Cultured Cells	--
25	chr7:27954600-27962600	Weak transcription	Right Ventricle	heart
26	chr7:27954600-27963000	Weak transcription	Left Ventricle	heart
27	chr7:27955000-27956200	Weak transcription	Primary B cells from cord blood	blood
28	chr7:27955000-27956600	Weak transcription	Colon Smooth Muscle	Colon
29	chr7:27955200-27956400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr7:27955200-27958400	Weak transcription	HUES64 Cell Line	embryonic stem cell
31	chr7:27955200-27962600	Weak transcription	Fetal Muscle Trunk	muscle
32	chr7:27955600-27957000	Enhancers	A549	lung
33	chr7:27955800-27960800	Weak transcription	Rectal Mucosa Donor 31	rectum
34	chr7:27956000-27956400	ZNF genes & repeats	Brain Hippocampus Middle	brain
35	chr7:27956000-27957200	Strong transcription	Monocytes-CD14+_RO01746	blood
36	chr7:27956000-27957600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr7:27956000-27957800	Enhancers	HMEC	breast
38	chr7:27956000-27958000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr7:27956000-27958000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr7:27956000-27958400	Enhancers	NHEK	skin

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