Variant report

Variant	rs200
Chromosome Location	chr7:27946855-27946856
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	chr7:27778531..27781161-chr7:27946249..27948488,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000106052	Chromatin interaction
ENSG00000229893	Chromatin interaction

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

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

rs_ID	r²[population]
rs10249314	0.85[CEU][hapmap]
rs10951187	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11763181	0.85[CEU][hapmap]
rs12538288	0.85[CEU][hapmap];1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1859109	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs191	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs197	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs201	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs205	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs207	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs208	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2097737	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs211	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs213	1.00[CEU][hapmap]
rs214	1.00[AFR][1000 genomes]
rs215	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2158892	0.87[CEU][hapmap]
rs218	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4722746	0.85[CEU][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6462060	0.85[CEU][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6951040	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6958293	0.82[CEU][hapmap];1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6968362	0.85[CEU][hapmap]
rs6968677	0.85[CEU][hapmap]
rs6969949	1.00[CEU][hapmap]
rs6970113	0.85[CEU][hapmap];1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6970160	0.85[CEU][hapmap]
rs6972944	0.85[CEU][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs73083394	0.94[EUR][1000 genomes]
rs7778340	0.85[CEU][hapmap];1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7783410	0.85[CEU][hapmap];1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7787507	0.85[CEU][hapmap];1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs916854	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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

No data

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:27926600-27956000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr7:27930000-27949800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr7:27937600-27953800	Weak transcription	Right Ventricle	heart
4	chr7:27937600-27956200	Weak transcription	Gastric	stomach
5	chr7:27939200-27953000	Weak transcription	Left Ventricle	heart
6	chr7:27939800-27950200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr7:27939800-27950400	Weak transcription	Pancreas	Pancrea
8	chr7:27941200-27954400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr7:27941200-27956200	Weak transcription	Aorta	Aorta
10	chr7:27941400-27949800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr7:27941400-27957600	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr7:27941400-27990800	Weak transcription	Primary T cells from cord blood	blood
13	chr7:27941600-27947400	Weak transcription	Fetal Lung	lung
14	chr7:27941600-27956000	Weak transcription	Brain Hippocampus Middle	brain
15	chr7:27941600-27962800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr7:27942200-27949800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr7:27942200-27950000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr7:27942200-27953800	Weak transcription	Stomach Smooth Muscle	stomach
19	chr7:27942200-27956000	Weak transcription	Monocytes-CD14+_RO01746	blood
20	chr7:27942400-27952400	Weak transcription	Primary B cells from cord blood	blood
21	chr7:27942400-28005600	Weak transcription	Primary monocytes fromperipheralblood	blood
22	chr7:27943600-27948000	Weak transcription	Primary B cells from peripheral blood	blood
23	chr7:27943800-27947200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr7:27945200-27948800	Enhancers	HUES64 Cell Line	embryonic stem cell
25	chr7:27945600-27948400	Enhancers	HUES6 Cell Line	embryonic stem cell
26	chr7:27945600-27948800	Enhancers	ES-I3 Cell Line	embryonic stem cell
27	chr7:27945600-27948800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
28	chr7:27945600-27949000	Enhancers	H1 Cell Line	embryonic stem cell
29	chr7:27945600-27949600	Enhancers	iPS-18 Cell Line	embryonic stem cell
30	chr7:27945600-27949800	Enhancers	iPS-15b Cell Line	embryonic stem cell
31	chr7:27945800-27947200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr7:27945800-27948400	Enhancers	H9 Cell Line	embryonic stem cell
33	chr7:27946000-27949600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr7:27946000-27949800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
35	chr7:27946000-27952400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
36	chr7:27946400-27947200	Enhancers	iPS-20b Cell Line	embryonic stem cell
37	chr7:27946400-27948400	Enhancers	ES-WA7 Cell Line	embryonic stem cell
38	chr7:27946600-27949600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr7:27946600-27949800	Enhancers	HUES48 Cell Line	embryonic stem cell
40	chr7:27946600-27953400	Weak transcription	Rectal Smooth Muscle	rectum
41	chr7:27946800-27949800	Weak transcription	NHDF-Ad	bronchial
42	chr7:27946800-27953400	Weak transcription	Colon Smooth Muscle	Colon

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links