Variant report

Variant	rs9403828
Chromosome Location	chr6:147222516-147222517
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:147221999..147224137-chr6:147543696..147547016,3	MCF-7	breast:
2	chr6:147221492..147224047-chr6:147523320..147525428,2	K562	blood:
3	chr6:147222495..147225240-chr6:147606408..147608326,2	K562	blood:
4	chr6:147221960..147224216-chr6:147538711..147540256,2	MCF-7	breast:
5	chr6:147222414..147228613-chr6:147523028..147527280,11	MCF-7	breast:
6	chr6:147222212..147229913-chr6:147522379..147526472,14	MCF-7	breast:
7	chr6:147221788..147226460-chr6:147542201..147549451,7	K562	blood:
8	chr6:147221766..147223377-chr6:147555409..147557127,2	K562	blood:
9	chr6:147220668..147222971-chr6:147322912..147325249,2	K562	blood:
10	chr6:147222438..147225404-chr6:147523543..147527652,4	K562	blood:

No data

No data

No data

Extended variants
information (count: 10 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs1998641	0.88[CEU][hapmap];0.80[CHB][hapmap];0.82[CHD][hapmap];0.94[JPT][hapmap];0.83[MEX][hapmap];0.83[ASN][1000 genomes]
rs4895704	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];0.97[GIH][hapmap];0.89[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs724774	0.80[CEU][hapmap];0.80[CHB][hapmap];0.94[JPT][hapmap];0.83[ASN][1000 genomes]
rs912577	1.00[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9377035	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9390435	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9399589	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9399590	0.92[CEU][hapmap];0.80[CHB][hapmap];0.94[JPT][hapmap]
rs9403825	0.86[ASW][hapmap];0.92[CEU][hapmap];0.95[CHB][hapmap];0.87[CHD][hapmap];0.97[GIH][hapmap];0.88[JPT][hapmap];0.96[MEX][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830838	chr6:147090745-147274669	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9403828	KATNA1	cis	parietal	SCAN
rs9403828	RAB32	cis	cerebellum	SCAN

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:147215200-147224200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr6:147216000-147224600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr6:147218000-147225800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr6:147218200-147226600	Weak transcription	NHLF	lung
5	chr6:147219800-147223800	Weak transcription	Primary hematopoietic stem cells	blood
6	chr6:147220000-147223200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
7	chr6:147220400-147223800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr6:147220600-147223200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr6:147221400-147224800	Enhancers	K562	blood
10	chr6:147222000-147226000	Weak transcription	Stomach Smooth Muscle	stomach

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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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