Variant report

Variant	rs7668401
Chromosome Location	chr4:48491442-48491443
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:48489612..48492154-chr4:48493154..48495602,2	K562	blood:

Extended variants
information (count: 25 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10031120	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10517217	0.80[JPT][hapmap]
rs1055721	0.85[JPT][hapmap]
rs10938532	0.83[AMR][1000 genomes]
rs10938533	0.81[ASN][1000 genomes]
rs13125511	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17472113	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1996422	0.86[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.83[YRI][hapmap]
rs4413478	0.88[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.93[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6447631	0.85[JPT][hapmap]
rs6812622	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6827019	0.87[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs7340880	0.90[ASN][1000 genomes]
rs7655066	0.85[JPT][hapmap]
rs7664981	0.94[JPT][hapmap]
rs7688310	0.85[JPT][hapmap]
rs7694862	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9992736	0.85[JPT][hapmap]
rs9993088	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9999482	0.85[JPT][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	nsv470034	chr4:48427773-48605628	Strong transcription Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
2	nsv594121	chr4:48427773-48605628	Bivalent/Poised TSS Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
3	nsv829925	chr4:48467693-48639342	Weak transcription Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent Enhancer Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv879008	chr4:48473439-48496804	Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
5	nsv879009	chr4:48476539-48494546	Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7668401	SLAIN2	cis	parietal	SCAN
rs7668401	SLAIN2	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:48486200-48492000	Weak transcription	Aorta	Aorta
2	chr4:48486600-48491800	Weak transcription	Pancreas	Pancrea
3	chr4:48487200-48505800	Weak transcription	A549	lung
4	chr4:48489600-48491600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr4:48491200-48491600	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
6	chr4:48491400-48491600	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
7	chr4:48491400-48493000	Transcr. at gene 5' and 3'	Cortex derived primary cultured neurospheres	brain
8	chr4:48491400-48493800	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
9	chr4:48491400-48494400	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
10	chr4:48491400-48495400	Weak transcription	K562	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links