Variant report

Variant	rs7864844
Chromosome Location	chr9:18905134-18905135
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	TEAD4	chr9:18905130-18905931	SK-N-SH	brain:	n/a	chr9:18905464-18905473
2	GATA3	chr9:18905130-18905821	SK-N-SH	brain:	n/a	n/a

Variant related genes	Relation type
ADAMTSL1	TF binding region

Extended variants
information (count: 21 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10963829	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1433830	0.84[CEU][hapmap];0.81[JPT][hapmap]
rs1897725	0.81[JPT][hapmap]
rs2099392	0.80[JPT][hapmap]
rs35188448	0.90[ASN][1000 genomes]
rs55653217	0.90[ASN][1000 genomes]
rs56401921	0.83[ASN][1000 genomes]
rs7029205	0.81[JPT][hapmap]
rs7030876	0.90[ASN][1000 genomes]
rs7032286	0.81[CEU][hapmap];0.81[JPT][hapmap]
rs7861285	0.83[ASN][1000 genomes]
rs7861391	0.85[ASN][1000 genomes]
rs7864728	0.90[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	nsv491807	chr9:18243672-19009770	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv525659	chr9:18288212-19009041	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	nsv1019127	chr9:18288271-18996288	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
4	nsv892692	chr9:18519699-19045502	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
5	nsv949111	chr9:18758205-18994588	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases
6	nsv892698	chr9:18830444-18905289	Genic enhancers Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
7	nsv1017820	chr9:18882219-19587377	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	94 gene(s)	inside rSNPs	diseases
8	nsv540078	chr9:18882219-19587377	Genic enhancers Transcr. at gene 5' and 3' Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	94 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7864844	RRAGA	cis	lymphoblastoid	seeQTL
rs7864844	PSIP1	cis	cerebellum	SCAN
rs7864844	IFNB1	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:18894800-18909200	Weak transcription	Fetal Heart	heart
2	chr9:18896800-18910600	Weak transcription	Stomach Smooth Muscle	stomach
3	chr9:18897000-18905200	Weak transcription	NHLF	lung
4	chr9:18897000-18910600	Weak transcription	Duodenum Smooth Muscle	Duodenum
5	chr9:18897200-18905600	Weak transcription	Aorta	Aorta
6	chr9:18897400-18920400	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr9:18897600-18906600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr9:18898200-18905600	Weak transcription	Fetal Stomach	stomach
9	chr9:18898400-18905200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr9:18903000-18909400	Enhancers	Fetal Thymus	thymus
11	chr9:18903400-18906600	Weak transcription	Fetal Muscle Leg	muscle
12	chr9:18904400-18905600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr9:18904600-18905800	Enhancers	Osteobl	bone
14	chr9:18904800-18905200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr9:18904800-18905200	Genic enhancers	HSMM	muscle
16	chr9:18904800-18905600	Enhancers	Muscle Satellite Cultured Cells	--
17	chr9:18904800-18907400	Enhancers	NH-A	brain
18	chr9:18904800-18908000	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr9:18905000-18905400	Enhancers	NHDF-Ad	bronchial
20	chr9:18905000-18906000	Enhancers	HSMMtube	muscle
21	chr9:18905000-18906200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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