Variant report

Variant	rs1313772
Chromosome Location	chr4:3058583-3058584
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	chr4:3057371..3060027-chr4:3074325..3077279,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000197386	Chromatin interaction
ENSG00000251075	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs1263308	0.95[ASN][1000 genomes]
rs1263309	0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1313766	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1313767	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1313769	0.99[ASN][1000 genomes]
rs1313770	1.00[ASN][1000 genomes]
rs1313773	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1313774	1.00[ASN][1000 genomes]
rs2067003	0.96[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2471334	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2798285	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2798289	0.98[ASN][1000 genomes]
rs2798296	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.91[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2798297	0.83[ASN][1000 genomes]
rs2857843	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2857846	0.98[ASN][1000 genomes]
rs2857847	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2857853	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2857936	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3021126	0.82[ASW][hapmap];0.92[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3418626	chr4:2741174-3461492	Genic enhancers Weak transcription Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	esv3397632	chr4:2741239-3460583	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Strong transcription Bivalent Enhancer 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 miRNA target site	63 gene(s)	inside rSNPs	diseases
3	nsv461163	chr4:2906285-3234980	Enhancers Strong transcription Flanking Active TSS Genic enhancers Weak transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	52 gene(s)	inside rSNPs	diseases
4	nsv593437	chr4:2906285-3234980	Genic enhancers Active TSS Strong transcription Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	52 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1313772	GRK4	cis	cerebellum	SCAN
rs1313772	RGS12	cis	parietal	SCAN

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:3048200-3075200	Weak transcription	Right Atrium	heart
2	chr4:3049600-3074800	Weak transcription	Lung	lung
3	chr4:3053800-3064600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr4:3057000-3058800	ZNF genes & repeats	Primary B cells from peripheral blood	blood
5	chr4:3057800-3058800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr4:3058200-3060000	Weak transcription	Primary B cells from cord blood	blood
7	chr4:3058200-3060400	Weak transcription	Adipose Nuclei	Adipose
8	chr4:3058200-3075200	Weak transcription	Psoas Muscle	Psoas
9	chr4:3058400-3059600	Weak transcription	Monocytes-CD14+_RO01746	blood
10	chr4:3058400-3060200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr4:3058400-3060600	Weak transcription	Skeletal Muscle Male	skeletal muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links