Variant report

Variant	rs4945176
Chromosome Location	chr11:77236132-77236133
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 15 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs1540180	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4572159	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4945179	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4945181	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs58219609	0.87[EUR][1000 genomes]
rs6592726	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 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	esv3424135	chr11:76961603-77277087	Strong transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Enhancers Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
6	nsv1037724	chr11:77061945-77250391	Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	nsv541091	chr11:77061945-77250391	Weak transcription Active TSS Enhancers Strong transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
8	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
9	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
rs4945176	INTS4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:77223200-77240600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr11:77233600-77236600	Weak transcription	HUES48 Cell Line	embryonic stem cell
3	chr11:77233600-77236600	Weak transcription	HUES6 Cell Line	embryonic stem cell
4	chr11:77233600-77236800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr11:77233600-77237000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr11:77234600-77236600	Enhancers	Brain Substantia Nigra	brain
7	chr11:77234800-77237400	Enhancers	Brain Hippocampus Middle	brain
8	chr11:77235200-77236600	Enhancers	Brain Cingulate Gyrus	brain
9	chr11:77235200-77237200	Enhancers	ES-I3 Cell Line	embryonic stem cell
10	chr11:77235600-77236600	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr11:77235600-77236600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr11:77235600-77236600	Weak transcription	Brain Angular Gyrus	brain
13	chr11:77235600-77237000	Weak transcription	Brain Anterior Caudate	brain
14	chr11:77235800-77236200	Weak transcription	HUES64 Cell Line	embryonic stem cell
15	chr11:77235800-77236200	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr11:77235800-77236400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
17	chr11:77235800-77236600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr11:77235800-77240600	Weak transcription	H1 Cell Line	embryonic stem cell
19	chr11:77236000-77236400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
20	chr11:77236000-77236400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain

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