Variant report

Variant	rs4976783
Chromosome Location	chr5:177901202-177901203
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:177892314..177894580-chr5:177899757..177901738,2	K562	blood:

Extended variants
information (count: 38 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10039491	0.86[ASW][hapmap];0.86[YRI][hapmap]
rs10040117	0.81[EUR][1000 genomes]
rs10060223	0.85[JPT][hapmap]
rs10069282	0.93[GIH][hapmap];0.85[JPT][hapmap];0.87[TSI][hapmap]
rs11249547	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[JPT][hapmap];0.86[MEX][hapmap];0.85[TSI][hapmap];0.84[YRI][hapmap];0.84[AMR][1000 genomes]
rs11249804	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11249805	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12153215	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2546646	0.85[CHD][hapmap];0.85[JPT][hapmap]
rs2617265	1.00[JPT][hapmap]
rs2672816	0.85[CHD][hapmap];0.85[JPT][hapmap]
rs2672818	0.85[CHD][hapmap];0.85[JPT][hapmap]
rs2672826	0.85[JPT][hapmap]
rs2840140	0.90[GIH][hapmap];0.85[JPT][hapmap]
rs4976731	0.81[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.84[AMR][1000 genomes]
rs4976780	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs55768745	0.84[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs56108725	0.84[AMR][1000 genomes]
rs56137206	0.84[AMR][1000 genomes]
rs686282	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs6884035	1.00[CHB][hapmap];0.88[YRI][hapmap];0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs952086	1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.97[MKK][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948342	chr5:177384542-178168737	Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Strong transcription Weak transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	141 gene(s)	inside rSNPs	diseases
2	nsv1029398	chr5:177502106-178070654	Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	136 gene(s)	inside rSNPs	diseases
3	nsv1024689	chr5:177638936-177926244	Enhancers Bivalent Enhancer Weak transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
4	nsv537968	chr5:177638936-177926244	Bivalent Enhancer Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
5	nsv427739	chr5:177766033-177966666	Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	nsv883210	chr5:177771925-177980792	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
7	nsv883213	chr5:177811754-177947771	Enhancers Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
8	nsv462570	chr5:177860454-178010145	Bivalent Enhancer Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
9	nsv600423	chr5:177860454-178010145	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Strong transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
10	nsv1029822	chr5:177872333-177931889	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
11	nsv1033039	chr5:177873974-177926244	Enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
12	nsv537971	chr5:177873974-177926244	Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
13	nsv883214	chr5:177876309-178047217	Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Weak transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
14	nsv1030915	chr5:177880081-177934927	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
15	nsv462571	chr5:177898650-177961860	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
16	nsv600424	chr5:177898650-177961860	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4976783	RAB24	cis	parietal	SCAN
rs4976783	ZNF354A	cis	cerebellum	SCAN
rs4976783	CLTB	cis	parietal	SCAN

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:177890600-177901600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
2	chr5:177894600-177902000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr5:177895200-177901600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr5:177896000-177903600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr5:177898800-177902600	Weak transcription	Spleen	Spleen
6	chr5:177899000-177901600	Weak transcription	HUES64 Cell Line	embryonic stem cell
7	chr5:177899000-177910400	Weak transcription	Thymus	Thymus
8	chr5:177899200-177901800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr5:177899400-177902200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr5:177899600-177907400	Enhancers	Primary monocytes fromperipheralblood	blood
11	chr5:177900400-177901400	Enhancers	Fetal Thymus	thymus
12	chr5:177900600-177904000	Enhancers	Primary neutrophils fromperipheralblood	blood
13	chr5:177900800-177901400	Enhancers	Dnd41	blood
14	chr5:177901000-177901400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr5:177901000-177901400	Enhancers	Cortex derived primary cultured neurospheres	brain
16	chr5:177901000-177902200	Enhancers	HUES48 Cell Line	embryonic stem cell
17	chr5:177901200-177901400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr5:177901200-177902200	Enhancers	Liver	Liver
19	chr5:177901200-177904000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr5:177901200-177904000	Enhancers	Monocytes-CD14+_RO01746	blood

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