Variant report

Variant	rs7854969
Chromosome Location	chr9:7961157-7961158
allele	C/T
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	POLR2A	chr9:7961127-7961224	GM12878	blood:	n/a	n/a

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-KDM4C-7	chr9:7960826-7961234	XLOC_007279
2	lnc-C9orf123-4	chr9:7960830-7961188	NONHSAT130186

Variant related genes	Relation type
ENSG00000231902	TF binding region

Extended variants
information (count: 17 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs59429921	1.00[AMR][1000 genomes]
rs60687579	1.00[AMR][1000 genomes]
rs7018764	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73640565	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73640569	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73640570	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73640571	1.00[AMR][1000 genomes]
rs73640572	0.84[AFR][1000 genomes];1.00[AMR][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	nsv1033077	chr9:7358832-7990735	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
2	nsv539977	chr9:7358832-7990735	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
3	nsv995116	chr9:7682729-8065192	Strong transcription Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	nsv8414	chr9:7827373-8511613	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
5	nsv1024456	chr9:7887727-8157591	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
6	nsv539979	chr9:7887727-8157591	Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
7	nsv892216	chr9:7910934-7985651	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region lncRNA	6 gene(s)	inside rSNPs	diseases
8	nsv892217	chr9:7919153-7978514	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region lncRNA	6 gene(s)	inside rSNPs	diseases
9	nsv892218	chr9:7929372-7964559	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Active TSS	TF binding region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:7958400-7961400	Enhancers	Fetal Thymus	thymus
2	chr9:7958600-7962600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr9:7958800-7961400	Enhancers	Thymus	Thymus
4	chr9:7959000-7962200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr9:7959400-7962600	Enhancers	Fetal Heart	heart
6	chr9:7959800-7961200	Enhancers	Primary neutrophils fromperipheralblood	blood
7	chr9:7959800-7961400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr9:7959800-7962600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr9:7959800-7967200	Weak transcription	Dnd41	blood
10	chr9:7960200-7961600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr9:7960400-7963600	Enhancers	Sigmoid Colon	Sigmoid Colon
12	chr9:7960600-7961200	Enhancers	Fetal Lung	lung
13	chr9:7960600-7961400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr9:7960600-7961400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr9:7960600-7961600	Enhancers	iPS-18 Cell Line	embryonic stem cell
16	chr9:7960600-7963200	Enhancers	Rectal Mucosa Donor 31	rectum
17	chr9:7960800-7961400	Enhancers	HUES64 Cell Line	embryonic stem cell
18	chr9:7960800-7961400	Enhancers	iPS-20b Cell Line	embryonic stem cell
19	chr9:7961000-7961800	Enhancers	Stomach Mucosa	stomach
20	chr9:7961000-7962800	Enhancers	Fetal Brain Male	brain
21	chr9:7961000-7964000	Enhancers	Rectal Mucosa Donor 29	rectum
22	chr9:7961000-7967200	Weak transcription	Primary T cells from cord blood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links