Variant report

Variant	rs7850989
Chromosome Location	chr9:14541236-14541237
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 11 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs10961558	0.84[ASN][1000 genomes]
rs2149103	0.84[ASN][1000 genomes]
rs4741396	0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1029491	chr9:14033607-14942373	Enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	nsv915804	chr9:14182608-14903050	Enhancers Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
3	nsv916811	chr9:14210978-14542068	Enhancers Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
4	nsv831517	chr9:14512924-14738206	Enhancers Genic enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv892604	chr9:14519301-14559910	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	nsv613637	chr9:14524438-15011915	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
7	nsv613638	chr9:14539758-14550138	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
8	nsv613639	chr9:14539758-14552236	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7850989	FAT2	trans	cerebellum	SCAN
rs7850989	C9orf93	cis	parietal	SCAN

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:14535400-14541600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr9:14535400-14542200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr9:14537600-14547600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr9:14538800-14541400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
5	chr9:14538800-14541400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr9:14538800-14541600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr9:14538800-14541600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr9:14539200-14542600	Weak transcription	K562	blood
9	chr9:14541000-14543200	Enhancers	iPS-18 Cell Line	embryonic stem cell
10	chr9:14541200-14542800	Enhancers	HUES6 Cell Line	embryonic stem cell
11	chr9:14541200-14542800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr9:14541200-14543000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr9:14541200-14543000	Enhancers	H9 Cell Line	embryonic stem cell
14	chr9:14541200-14543000	Enhancers	HUES64 Cell Line	embryonic stem cell
15	chr9:14541200-14543000	Enhancers	iPS-15b Cell Line	embryonic stem cell
16	chr9:14541200-14543200	Enhancers	H1 Cell Line	embryonic stem cell
17	chr9:14541200-14543200	Enhancers	HUES48 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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