Variant report

Variant	rs11699743
Chromosome Location	chr20:24114150-24114151
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr20:24111886..24113648-chr20:24113789..24115599,2	MCF-7	breast:
2	chr20:24112072..24114906-chr20:24115605..24118020,3	MCF-7	breast:
3	chr20:24113587..24115337-chr20:24123688..24125826,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000236151	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs1005527	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1012783	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1123671	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11696686	0.83[EUR][1000 genomes]
rs11697353	0.91[ASN][1000 genomes]
rs12480224	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17249809	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1884519	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2070275	0.81[ASN][1000 genomes]
rs2103922	0.89[EUR][1000 genomes]
rs35663453	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs55921601	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6132695	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6132696	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6138201	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6138207	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6138210	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6138214	0.81[EUR][1000 genomes]
rs61657263	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7270353	0.81[CHB][hapmap];0.93[CHD][hapmap];0.82[GIH][hapmap];0.82[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv9793	chr20:23939613-24734850	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	esv3328348	chr20:24095746-24285830	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Genic enhancers	TF binding region Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11699743	INSM1	cis	parietal	SCAN
rs11699743	CST8	cis	cerebellum	SCAN

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:24111000-24117200	Enhancers	Placenta Amnion	Placenta Amnion
2	chr20:24111400-24117200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr20:24111400-24120400	Enhancers	Placenta	Placenta
4	chr20:24111600-24115800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr20:24111600-24119600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr20:24111800-24115600	Enhancers	HMEC	breast
7	chr20:24111800-24116400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr20:24112000-24115000	Weak transcription	HUES48 Cell Line	embryonic stem cell
9	chr20:24112200-24114800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr20:24112800-24115000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr20:24113000-24114800	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr20:24113000-24114800	Weak transcription	HUES6 Cell Line	embryonic stem cell
13	chr20:24113000-24114800	Weak transcription	Esophagus	oesophagus
14	chr20:24113000-24114800	Weak transcription	HUVEC	blood vessel
15	chr20:24113000-24115000	Weak transcription	Primary T cells fromperipheralblood	blood
16	chr20:24113000-24115000	Weak transcription	Pancreas	Pancrea
17	chr20:24113000-24117600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr20:24113200-24114800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
19	chr20:24113200-24116000	Enhancers	NHEK	skin
20	chr20:24113400-24114400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr20:24113600-24115000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
22	chr20:24113800-24115000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links