Variant report

Variant	rs687228
Chromosome Location	chr11:121364963-121364964
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	chr11:121358992..121360735-chr11:121362875..121365300,2	MCF-7	breast:

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

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs12364988	0.81[EUR][1000 genomes]
rs12798073	0.93[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1784927	0.89[CEU][hapmap];0.86[EUR][1000 genomes]
rs1784934	0.87[JPT][hapmap]
rs4936632	0.86[JPT][hapmap]
rs523917	1.00[CEU][hapmap];0.92[CHB][hapmap];0.91[JPT][hapmap];0.84[YRI][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs550469	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs560573	0.89[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs593769	0.89[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs596437	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs599161	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs624310	0.89[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs633197	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs641120	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs645275	0.91[JPT][hapmap]
rs652067	0.89[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs656338	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs662821	0.85[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];0.96[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs668387	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs676759	0.89[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs681970	0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs689021	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs693855	0.90[CHB][hapmap];0.82[JPT][hapmap];0.88[ASN][1000 genomes]
rs923892	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs923893	0.80[CEU][hapmap];0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv898427	chr11:121299288-121411041	Strong transcription Flanking Bivalent TSS/Enh Weak transcription Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv522474	chr11:121356968-121436270	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	nsv975233	chr11:121359656-121574786	Genic enhancers Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:91 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:121349800-121365000	Weak transcription	Cortex derived primary cultured neurospheres	brain
2	chr11:121349800-121393000	Weak transcription	Colonic Mucosa	Colon
3	chr11:121350000-121401400	Weak transcription	Fetal Brain Male	brain
4	chr11:121350200-121367800	Weak transcription	Fetal Kidney	kidney
5	chr11:121350400-121393200	Weak transcription	Gastric	stomach
6	chr11:121350800-121368400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr11:121351200-121366600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr11:121351400-121384600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr11:121352800-121377600	Strong transcription	HepG2	liver
10	chr11:121353600-121367200	Weak transcription	Fetal Lung	lung
11	chr11:121353600-121377000	Weak transcription	Pancreas	Pancrea
12	chr11:121353800-121365000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr11:121353800-121365000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr11:121353800-121374200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr11:121354200-121365000	Weak transcription	HMEC	breast
16	chr11:121354400-121365000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr11:121354600-121365000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr11:121355600-121365000	Strong transcription	Monocytes-CD14+_RO01746	blood
19	chr11:121356000-121365000	Strong transcription	Primary neutrophils fromperipheralblood	blood
20	chr11:121358800-121366800	Weak transcription	Rectal Smooth Muscle	rectum
21	chr11:121358800-121367400	Weak transcription	Stomach Smooth Muscle	stomach
22	chr11:121359000-121365800	Weak transcription	Brain Angular Gyrus	brain
23	chr11:121359000-121367800	Weak transcription	Brain Substantia Nigra	brain
24	chr11:121359200-121365000	Weak transcription	H9 Cell Line	embryonic stem cell
25	chr11:121359200-121365000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
26	chr11:121359200-121365200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr11:121359200-121365200	Weak transcription	Brain Inferior Temporal Lobe	brain
28	chr11:121359200-121367600	Weak transcription	Brain Cingulate Gyrus	brain
29	chr11:121359200-121367600	Weak transcription	Ovary	ovary
30	chr11:121359200-121367800	Weak transcription	Aorta	Aorta
31	chr11:121359200-121369800	Weak transcription	Left Ventricle	heart
32	chr11:121359200-121384200	Weak transcription	Fetal Stomach	stomach
33	chr11:121359400-121367400	Weak transcription	Brain Anterior Caudate	brain
34	chr11:121359400-121367600	Weak transcription	Colon Smooth Muscle	Colon
35	chr11:121359600-121365000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
36	chr11:121359600-121367800	Weak transcription	Spleen	Spleen
37	chr11:121359800-121365000	Weak transcription	Stomach Mucosa	stomach
38	chr11:121359800-121365600	Weak transcription	Thymus	Thymus
39	chr11:121359800-121377000	Weak transcription	Esophagus	oesophagus
40	chr11:121360200-121365000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr11:121360600-121367000	Weak transcription	Pancreatic Islets	Pancreatic Islet
42	chr11:121360600-121368400	Weak transcription	Brain Germinal Matrix	brain
43	chr11:121360800-121365000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr11:121360800-121365000	Weak transcription	NHEK	skin
45	chr11:121360800-121367600	Weak transcription	Sigmoid Colon	Sigmoid Colon
46	chr11:121360800-121369800	Weak transcription	Brain Hippocampus Middle	brain
47	chr11:121360800-121384400	Weak transcription	Skeletal Muscle Female	skeletal muscle
48	chr11:121361000-121365000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr11:121362000-121365000	Weak transcription	Fetal Intestine Small	intestine
50	chr11:121362000-121367600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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