Variant report

Variant	rs13302749
Chromosome Location	chr9:6171731-6171732
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 26 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10118776	0.81[AMR][1000 genomes]
rs13283694	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13284060	1.00[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs13285109	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13291323	1.00[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs13293142	1.00[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs13296741	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13298301	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13301448	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs13302358	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs34110711	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs34282845	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs66887324	1.00[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs67923960	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948847	chr9:5712626-6417677	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	nsv1031086	chr9:5806949-6630686	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
3	nsv539967	chr9:5806949-6630686	Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
4	nsv613205	chr9:6032924-6332901	Flanking Active TSS Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv916394	chr9:6055497-6322471	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv892157	chr9:6093790-6322415	Weak transcription Enhancers Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv933124	chr9:6099101-6644738	Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
8	nsv831496	chr9:6101763-6285088	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
9	nsv521598	chr9:6142157-6291125	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
10	nsv892158	chr9:6149006-6266440	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
11	nsv1027270	chr9:6152434-6328227	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
12	nsv539968	chr9:6152434-6328227	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13302749	C9orf38	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:6160200-6173600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr9:6170600-6172000	Enhancers	Fetal Kidney	kidney
3	chr9:6170800-6172800	Enhancers	HUES64 Cell Line	embryonic stem cell
4	chr9:6170800-6172800	Enhancers	iPS-18 Cell Line	embryonic stem cell
5	chr9:6171000-6172600	Enhancers	HUES48 Cell Line	embryonic stem cell
6	chr9:6171000-6172800	Enhancers	HUES6 Cell Line	embryonic stem cell
7	chr9:6171000-6172800	Enhancers	iPS-15b Cell Line	embryonic stem cell
8	chr9:6171000-6172800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
9	chr9:6171000-6172800	Enhancers	NHDF-Ad	bronchial
10	chr9:6171400-6172800	Enhancers	ES-I3 Cell Line	embryonic stem cell
11	chr9:6171600-6172000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
12	chr9:6171600-6172000	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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