Variant report

Variant	rs6040429
Chromosome Location	chr20:11188606-11188607
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	chr20:10654014..10656712-chr20:11187168..11189438,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000101384	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs1013499	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1884163	0.98[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1884164	0.98[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2207101	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2207412	0.98[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs4813965	0.93[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs6033055	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs6040430	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6078099	0.99[ASN][1000 genomes]
rs6104721	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs6108864	0.85[CHB][hapmap];0.87[JPT][hapmap];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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

No data

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:11185200-11190000	Enhancers	HMEC	breast
2	chr20:11185400-11189400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr20:11185400-11189600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr20:11185600-11189400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr20:11185600-11189600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr20:11186000-11197000	Weak transcription	HSMM	muscle
7	chr20:11186200-11188800	Weak transcription	Duodenum Mucosa	Duodenum
8	chr20:11186400-11192800	Weak transcription	Fetal Kidney	kidney
9	chr20:11186400-11193400	Weak transcription	HUES64 Cell Line	embryonic stem cell
10	chr20:11186600-11189200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr20:11186600-11197200	Weak transcription	Pancreas	Pancrea
12	chr20:11186800-11195200	Weak transcription	HUES6 Cell Line	embryonic stem cell
13	chr20:11186800-11197600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr20:11187800-11189600	Enhancers	Muscle Satellite Cultured Cells	--
15	chr20:11188000-11188800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr20:11188000-11189400	Flanking Active TSS	A549	lung
17	chr20:11188000-11189400	Enhancers	NH-A	brain
18	chr20:11188200-11189400	Enhancers	NHDF-Ad	bronchial
19	chr20:11188200-11189600	Enhancers	Fetal Intestine Large	intestine
20	chr20:11188200-11189600	Enhancers	Fetal Intestine Small	intestine
21	chr20:11188200-11189600	Enhancers	Osteobl	bone
22	chr20:11188400-11188800	Enhancers	Brain Anterior Caudate	brain
23	chr20:11188400-11188800	Enhancers	Brain Cingulate Gyrus	brain
24	chr20:11188400-11188800	Enhancers	Rectal Smooth Muscle	rectum
25	chr20:11188400-11189000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr20:11188400-11189000	Enhancers	HepG2	liver
27	chr20:11188400-11189200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr20:11188400-11189400	Enhancers	Duodenum Smooth Muscle	Duodenum
29	chr20:11188600-11188800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr20:11188600-11188800	Enhancers	Cortex derived primary cultured neurospheres	brain
31	chr20:11188600-11188800	Enhancers	Brain Hippocampus Middle	brain
32	chr20:11188600-11188800	Flanking Active TSS	NHEK	skin
33	chr20:11188600-11189200	Enhancers	Aorta	Aorta
34	chr20:11188600-11189200	Weak transcription	Small Intestine	intestine
35	chr20:11188600-11189400	Enhancers	Hela-S3	cervix
36	chr20:11188600-11189600	Enhancers	Stomach Mucosa	stomach
37	chr20:11188600-11190600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr20:11188600-11191200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links