Variant report

Variant	rs4946001
Chromosome Location	chr6:114766016-114766017
allele	A/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	GATA2	chr6:114765985-114766387	SH-SY5Y	brain:	n/a	chr6:114766171-114766181

Variant related genes	Relation type
ENSG00000228624	TF binding region

Extended variants
information (count: 59 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10080647	1.00[ASW][hapmap];1.00[JPT][hapmap];1.00[MKK][hapmap];0.84[ASN][1000 genomes]
rs10155761	0.83[ASN][1000 genomes]
rs1033885	0.85[CHB][hapmap];0.94[JPT][hapmap];0.83[ASN][1000 genomes]
rs11153481	0.97[ASN][1000 genomes]
rs11962755	0.81[ASN][1000 genomes]
rs11968668	0.81[JPT][hapmap]
rs12194487	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12200547	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1324441	0.85[CHB][hapmap];0.94[JPT][hapmap];0.83[ASN][1000 genomes]
rs1324446	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1324447	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1337330	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1337335	0.84[ASN][1000 genomes]
rs1337336	0.80[ASN][1000 genomes]
rs1408452	0.81[CHB][hapmap];0.88[JPT][hapmap]
rs1408453	0.81[CHB][hapmap];0.88[JPT][hapmap]
rs1408454	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17326650	0.81[ASN][1000 genomes]
rs2205734	0.97[ASN][1000 genomes]
rs2205737	0.81[ASN][1000 genomes]
rs2224692	0.85[JPT][hapmap]
rs2281012	0.81[JPT][hapmap]
rs2349468	0.81[ASN][1000 genomes]
rs2882172	0.81[ASN][1000 genomes]
rs4373385	0.85[ASN][1000 genomes]
rs4945515	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4945998	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4946003	0.82[JPT][hapmap]
rs56067384	0.81[ASN][1000 genomes]
rs6568838	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6568839	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6902333	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6902384	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6919491	0.81[ASN][1000 genomes]
rs6926249	0.81[ASN][1000 genomes]
rs6939817	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7749363	0.81[ASN][1000 genomes]
rs7754407	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9320491	0.81[ASN][1000 genomes]
rs9320493	1.00[ASW][hapmap];0.92[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[MKK][hapmap];0.92[TSI][hapmap];0.87[YRI][hapmap];0.92[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs9374461	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9374463	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9488390	0.84[ASN][1000 genomes]
rs9488391	0.81[ASN][1000 genomes]
rs9488397	0.80[ASN][1000 genomes]
rs9488404	0.83[JPT][hapmap]
rs9688943	0.83[JPT][hapmap]
rs969877	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv34434	chr6:114465305-115462799	Enhancers Weak transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
2	nsv464024	chr6:114489321-114837181	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
3	nsv604544	chr6:114489321-114837181	Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
4	esv3692910	chr6:114597419-115480580	Flanking Active TSS Enhancers Bivalent/Poised TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
5	nsv528128	chr6:114597657-115471129	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
6	nsv818451	chr6:114597657-115471129	Enhancers Bivalent/Poised TSS Bivalent Enhancer Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
7	nsv428494	chr6:114666307-114774841	Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
8	esv2758074	chr6:114666308-115526957	Enhancers Bivalent Enhancer Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
9	nsv1030191	chr6:114679497-115228028	Weak transcription Enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
10	nsv538424	chr6:114679497-115228028	Enhancers Flanking Active TSS Weak transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
11	nsv1025817	chr6:114715204-115006108	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4946001	RWDD1	cis	parietal	SCAN

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:114752400-114767200	Weak transcription	HUES6 Cell Line	embryonic stem cell
2	chr6:114752800-114770400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr6:114758400-114767000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr6:114762600-114767600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
5	chr6:114762600-114773800	Weak transcription	Psoas Muscle	Psoas
6	chr6:114765800-114766200	Enhancers	HUES64 Cell Line	embryonic stem cell
7	chr6:114765800-114766800	Enhancers	H1 Cell Line	embryonic stem cell
8	chr6:114766000-114766200	Bivalent Enhancer	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr6:114766000-114766400	Enhancers	iPS-20b Cell Line	embryonic stem cell
10	chr6:114766000-114767800	Enhancers	HUES48 Cell Line	embryonic stem cell
11	chr6:114766000-114770600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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