Variant report

Variant	rs4803659
Chromosome Location	chr19:44290235-44290236
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:43967500..43969727-chr19:44288135..44290383,3	MCF-7	breast:
2	chr19:44289645..44292572-chr19:44300661..44302875,2	MCF-7	breast:
3	chr19:44256760..44265122-chr19:44281375..44290996,18	K562	blood:
4	chr19:44256245..44259869-chr19:44284477..44291035,7	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-KCNN4-1	chr19:44289294-44290302	XLOC_013347

Variant related genes	Relation type
ENSG00000159871	Chromatin interaction
ENSG00000124466	Chromatin interaction
ENSG00000105771	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 6 )

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

rs_ID	r²[population]
rs10413172	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10416177	0.91[CHB][hapmap];0.91[CHD][hapmap];0.81[MEX][hapmap]
rs10422108	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11083724	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11547806	0.91[CHB][hapmap];0.81[JPT][hapmap]
rs11670159	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11673490	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12611428	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1386502	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.90[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3786956	0.85[CEU][hapmap];0.93[TSI][hapmap];0.83[EUR][1000 genomes]
rs4802200	0.88[AFR][1000 genomes]
rs61013802	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62116964	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67648499	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs67704568	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs68073292	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7251074	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8104300	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8109478	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8109812	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[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	nsv532821	chr19:43842383-44357315	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs4803659	ZNF350	cis	parietal	SCAN
rs4803659	IGFL2	cis	parietal	SCAN
rs4803659	KLK5	cis	parietal	SCAN
rs4803659	EMP3	cis	parietal	SCAN
rs4803659	KLK8	cis	cerebellum	SCAN
rs4803659	DHX34	cis	parietal	SCAN

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:44285400-44291400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr19:44287400-44291400	Enhancers	HMEC	breast
3	chr19:44289400-44302600	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr19:44289600-44290800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr19:44289600-44291000	Weak transcription	HSMM	muscle
6	chr19:44289600-44293000	Weak transcription	GM12878-XiMat	blood
7	chr19:44289600-44294800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
8	chr19:44289600-44295400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr19:44289800-44290400	Enhancers	Hela-S3	cervix
10	chr19:44289800-44290800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr19:44289800-44300800	Weak transcription	Placenta	Placenta
12	chr19:44290000-44302400	Weak transcription	NHEK	skin
13	chr19:44290200-44302200	Weak transcription	Breast Myoepithelial Primary Cells	Breast

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