Variant report

Variant	rs6078099
Chromosome Location	chr20:11186652-11186653
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	chr20:10676677..10677565-chr20:11185885..11186708,3	MCF-7	breast:

Extended variants
information (count: 17 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs1013499	0.99[ASN][1000 genomes]
rs1884163	0.96[ASN][1000 genomes]
rs1884164	0.96[ASN][1000 genomes]
rs2207101	0.99[ASN][1000 genomes]
rs2207412	0.96[ASN][1000 genomes]
rs4813965	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6033055	0.96[ASN][1000 genomes]
rs6040429	0.99[ASN][1000 genomes]
rs6040430	0.99[ASN][1000 genomes]
rs6104721	0.96[ASN][1000 genomes]
rs6108864	0.84[ASN][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	nsv1065969	chr20:10850562-11464172	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv544181	chr20:10850562-11464172	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers	TF binding region Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv585415	chr20:11134907-11383327	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv585416	chr20:11156775-11190087	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Active TSS Bivalent Enhancer	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv1056067	chr20:11174581-11213919	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	esv3381762	chr20:11186416-11186706	Weak transcription Enhancers Flanking Active TSS	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	chr20:11184400-11188600	Weak transcription	Aorta	Aorta
2	chr20:11185200-11188200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr20:11185200-11190000	Enhancers	HMEC	breast
4	chr20:11185400-11188200	Enhancers	NHEK	skin
5	chr20:11185400-11189400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr20:11185400-11189600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr20:11185600-11186800	Enhancers	Duodenum Smooth Muscle	Duodenum
8	chr20:11185600-11186800	Enhancers	Osteobl	bone
9	chr20:11185600-11187400	Enhancers	Cortex derived primary cultured neurospheres	brain
10	chr20:11185600-11188000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr20:11185600-11189400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr20:11185600-11189600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr20:11185800-11186800	Enhancers	Adipose Nuclei	Adipose
14	chr20:11185800-11186800	Enhancers	Fetal Intestine Small	intestine
15	chr20:11186000-11186800	Enhancers	HUES48 Cell Line	embryonic stem cell
16	chr20:11186000-11186800	Enhancers	HUES6 Cell Line	embryonic stem cell
17	chr20:11186000-11186800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr20:11186000-11186800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr20:11186000-11186800	Enhancers	Fetal Stomach	stomach
20	chr20:11186000-11187000	Enhancers	iPS-18 Cell Line	embryonic stem cell
21	chr20:11186000-11187400	Enhancers	Breast Myoepithelial Primary Cells	Breast
22	chr20:11186000-11197000	Weak transcription	HSMM	muscle
23	chr20:11186200-11188400	Weak transcription	Colon Smooth Muscle	Colon
24	chr20:11186200-11188400	Weak transcription	Rectal Smooth Muscle	rectum
25	chr20:11186200-11188600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr20:11186200-11188800	Weak transcription	Duodenum Mucosa	Duodenum
27	chr20:11186400-11187400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr20:11186400-11188000	Weak transcription	Stomach Mucosa	stomach
29	chr20:11186400-11188400	Weak transcription	Rectal Mucosa Donor 31	rectum
30	chr20:11186400-11192800	Weak transcription	Fetal Kidney	kidney
31	chr20:11186400-11193400	Weak transcription	HUES64 Cell Line	embryonic stem cell
32	chr20:11186600-11186800	Flanking Active TSS	A549	lung
33	chr20:11186600-11188000	Weak transcription	NH-A	brain
34	chr20:11186600-11188200	Weak transcription	Fetal Intestine Large	intestine
35	chr20:11186600-11188400	Weak transcription	Brain Anterior Caudate	brain
36	chr20:11186600-11188400	Weak transcription	Brain Cingulate Gyrus	brain
37	chr20:11186600-11188400	Weak transcription	Small Intestine	intestine
38	chr20:11186600-11188600	Weak transcription	Brain Hippocampus Middle	brain
39	chr20:11186600-11189200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr20:11186600-11197200	Weak transcription	Pancreas	Pancrea

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