Variant report

Variant	rs550098
Chromosome Location	chr1:197297408-197297409
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr1:197297300-197297450	HAc	cerebellar:	n/a	n/a
2	CTCF	chr1:197297395-197297454	HUVEC	blood vessel:	n/a	n/a
3	CTCF	chr1:197296842-197297467	A549	lung:	n/a	chr1:197297105-197297126 chr1:197297103-197297121 chr1:197297104-197297120
4	RAD21	chr1:197296778-197297656	SK-N-SH	brain:	n/a	chr1:197297104-197297123
5	CTCF	chr1:197296631-197297462	SK-N-SH	brain:	n/a	chr1:197297105-197297126 chr1:197297103-197297121 chr1:197297104-197297120

No.	Distal block	Cell Line	Cell type
1	chr1:197264828..197266996-chr1:197295003..197297632,2	MCF-7	breast:
2	chr1:197296323..197297408-chr1:197325745..197326738,7	MCF-7	breast:
3	chr1:197296672..197297586-chr1:197325782..197326703,4	K562	blood:

Variant related genes	Relation type
CRB1	TF binding region

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs1337169	0.95[CEU][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1415214	0.95[CEU][hapmap];0.91[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1615444	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1764622	0.85[CEU][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1764623	0.95[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1764624	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1764625	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1764786	1.00[CEU][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1764787	0.81[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs1764788	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1764791	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1764792	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1764800	0.91[YRI][hapmap]
rs2786108	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2786110	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2786111	1.00[CEU][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2786112	0.95[CEU][hapmap];0.84[YRI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2786113	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2786115	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2821127	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2821131	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs476390	0.88[YRI][hapmap]
rs482526	0.95[CEU][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs510135	0.88[YRI][hapmap]
rs518149	0.88[YRI][hapmap]
rs554009	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs570845	0.95[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs572447	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs580067	1.00[CEU][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs615647	0.88[YRI][hapmap]
rs616675	0.87[YRI][hapmap]
rs643025	1.00[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs658409	0.95[CEU][hapmap];0.92[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs664767	1.00[CEU][hapmap];0.92[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs675699	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][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	nsv528460	chr1:196542567-197446702	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers 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 miRNA target site	26 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:197290600-197297800	Weak transcription	Cortex derived primary cultured neurospheres	brain
2	chr1:197291000-197297800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr1:197296400-197298000	Enhancers	Brain Inferior Temporal Lobe	brain
4	chr1:197296400-197298200	Enhancers	Brain Hippocampus Middle	brain
5	chr1:197296800-197297800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr1:197296800-197298000	Enhancers	Brain Anterior Caudate	brain
7	chr1:197297000-197297600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr1:197297000-197298000	Enhancers	Brain Cingulate Gyrus	brain
9	chr1:197297400-197298000	Enhancers	Brain Germinal Matrix	brain
10	chr1:197297400-197298000	Enhancers	Brain Substantia Nigra	brain

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