Variant report

Variant	rs4846314
Chromosome Location	chr1:220498636-220498637
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 24 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10495146	0.89[MKK][hapmap]
rs10863546	0.90[ASN][1000 genomes]
rs12568631	0.83[EUR][1000 genomes]
rs1397959	0.82[MKK][hapmap]
rs1397960	0.89[MKK][hapmap]
rs17007514	0.96[ASN][1000 genomes]
rs17007533	0.86[ASN][1000 genomes]
rs2048479	0.89[MKK][hapmap]
rs2667965	0.81[EUR][1000 genomes]
rs4272630	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4846310	0.92[ASW][hapmap];1.00[CEU][hapmap];0.80[CHD][hapmap];0.91[GIH][hapmap];0.88[MEX][hapmap];0.85[TSI][hapmap];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4846626	0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6683491	0.89[MKK][hapmap]
rs6702901	0.88[ASN][1000 genomes]
rs7516304	0.92[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7524270	0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7532002	0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7534648	0.83[EUR][1000 genomes]
rs7545196	0.87[MKK][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1001681	chr1:220425057-220548325	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv535298	chr1:220425057-220548325	Weak transcription Strong transcription Genic enhancers Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv523114	chr1:220486349-220500958	Enhancers Weak transcription	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
4	nsv1006979	chr1:220488188-220501518	Enhancers Weak transcription	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
5	esv16878	chr1:220495388-220499568	Enhancers Weak transcription	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4846314	COL4A1	trans	lymphoblastoid	seeQTL

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:220493000-220499600	Weak transcription	Fetal Heart	heart
2	chr1:220495600-220498800	Weak transcription	GM12878-XiMat	blood
3	chr1:220498400-220498800	Enhancers	Primary hematopoietic stem cells short term culture	blood
4	chr1:220498400-220498800	Enhancers	Cortex derived primary cultured neurospheres	brain
5	chr1:220498400-220499000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr1:220498400-220499000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr1:220498400-220500200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived

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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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