Variant report

Variant	rs10899389
Chromosome Location	chr11:77281443-77281444
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 23 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10160677	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10793255	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10899386	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10899387	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10899394	0.87[ASN][1000 genomes]
rs11237215	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11237220	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11237225	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11512896	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11602520	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11823651	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2032395	0.89[ASN][1000 genomes]
rs4509797	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6592738	0.87[ASN][1000 genomes]
rs7129556	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs72945508	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7927173	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[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	nsv1048360	chr11:76900813-77387933	Strong transcription Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
2	nsv541089	chr11:76900813-77387933	Active TSS Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	nsv1049603	chr11:76900813-77520411	Strong transcription Weak transcription Active TSS Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
4	nsv541090	chr11:76900813-77520411	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
5	esv3437433	chr11:77101280-77291686	Flanking Bivalent TSS/Enh Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
6	esv2752651	chr11:77211136-77318279	Active TSS Flanking Active TSS Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10899389	INTS4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:77272400-77282600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr11:77278400-77282600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
3	chr11:77278400-77283000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
4	chr11:77279000-77281600	Enhancers	Ovary	ovary
5	chr11:77279200-77283800	Enhancers	Pancreas	Pancrea
6	chr11:77279400-77281600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr11:77279600-77284800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr11:77280000-77282800	Enhancers	Fetal Stomach	stomach
9	chr11:77280400-77282400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr11:77280400-77282400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr11:77280600-77281800	Weak transcription	HUES6 Cell Line	embryonic stem cell
12	chr11:77280600-77281800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr11:77280600-77282400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr11:77280600-77282400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr11:77280600-77282600	Weak transcription	H1 Cell Line	embryonic stem cell
16	chr11:77280600-77283000	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr11:77280800-77282600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr11:77280800-77282800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr11:77280800-77299600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr11:77281000-77283000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
21	chr11:77281400-77282600	Weak transcription	Fetal Muscle Trunk	muscle

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