Variant report

Variant	rs417353
Chromosome Location	chr6:4565355-4565356
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	chr6:4565116..4567008-chr6:4567329..4569157,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CDYL-12	chr6:4565221-4565484	NONHSAT107452

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs11754975	0.96[EUR][1000 genomes]
rs119194	0.96[EUR][1000 genomes]
rs13195583	0.96[EUR][1000 genomes]
rs1923318	0.96[EUR][1000 genomes]
rs2223634	0.80[EUR][1000 genomes]
rs366253	0.97[EUR][1000 genomes]
rs368513	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs379512	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs393589	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs415223	0.98[EUR][1000 genomes]
rs425229	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs429527	0.91[EUR][1000 genomes]
rs434509	0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs435655	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs437035	0.98[EUR][1000 genomes]
rs437061	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs438085	0.99[EUR][1000 genomes]
rs440354	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs441034	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs441797	0.94[EUR][1000 genomes]
rs451278	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4960003	0.96[EUR][1000 genomes]
rs651051	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7757235	0.82[EUR][1000 genomes]
rs84995	0.97[EUR][1000 genomes]
rs84997	0.97[EUR][1000 genomes]
rs9504148	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9504149	0.84[EUR][1000 genomes]
rs9504155	0.86[EUR][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	esv3421990	chr6:4446933-4659639	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv830576	chr6:4447554-4610604	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	esv3366530	chr6:4471528-4865322	ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv883415	chr6:4546491-4629654	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:4560000-4572400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr6:4562600-4566200	Enhancers	Fetal Muscle Leg	muscle
3	chr6:4563600-4566400	Weak transcription	NHEK	skin
4	chr6:4563800-4566800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr6:4564000-4565800	Enhancers	Fetal Muscle Trunk	muscle
6	chr6:4564000-4577800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr6:4564400-4566000	Enhancers	Brain Germinal Matrix	brain
8	chr6:4564600-4565800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr6:4564600-4566200	Enhancers	Cortex derived primary cultured neurospheres	brain
10	chr6:4564800-4565800	Enhancers	Fetal Stomach	stomach
11	chr6:4564800-4566000	Enhancers	Placenta	Placenta
12	chr6:4565000-4565400	Enhancers	Fetal Brain Female	brain
13	chr6:4565000-4565400	Enhancers	HSMMtube	muscle
14	chr6:4565000-4565600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr6:4565000-4565600	Enhancers	Adipose Nuclei	Adipose
16	chr6:4565000-4565600	Enhancers	Brain Hippocampus Middle	brain
17	chr6:4565000-4565600	Enhancers	Brain Substantia Nigra	brain
18	chr6:4565000-4565600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
19	chr6:4565000-4565800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr6:4565000-4565800	Enhancers	Brain Cingulate Gyrus	brain
21	chr6:4565000-4565800	Enhancers	Brain Inferior Temporal Lobe	brain
22	chr6:4565000-4566000	Enhancers	Brain Anterior Caudate	brain
23	chr6:4565000-4566000	Enhancers	Stomach Smooth Muscle	stomach
24	chr6:4565000-4568600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr6:4565200-4566000	Enhancers	Colon Smooth Muscle	Colon
26	chr6:4565200-4566400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links