Variant report

Variant	rs12734406
Chromosome Location	chr1:213000131-213000132
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	chr1:212782226..212783823-chr1:212998854..213001770,2	K562	blood:
2	chr1:212984776..212986773-chr1:212997927..213000551,2	K562	blood:

Variant related genes	Relation type
ENSG00000162772	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10494955	0.81[ASN][1000 genomes]
rs1054733	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10863999	0.81[ASN][1000 genomes]
rs10864000	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10864001	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11120026	0.81[ASN][1000 genomes]
rs11120027	0.81[ASN][1000 genomes]
rs11120032	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11120037	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11120039	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1133462	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12095846	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12097897	0.81[ASN][1000 genomes]
rs12126017	0.81[ASN][1000 genomes]
rs12130945	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12565557	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs12734543	0.88[ASN][1000 genomes]
rs12737398	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12741704	0.81[ASN][1000 genomes]
rs12744602	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2359322	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3820679	0.81[ASN][1000 genomes]
rs3862953	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4951463	0.81[ASN][1000 genomes]
rs6679350	0.81[ASN][1000 genomes]
rs6679549	0.81[ASN][1000 genomes]
rs6689604	0.86[ASN][1000 genomes]
rs6697507	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6700410	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6702611	0.81[ASN][1000 genomes]
rs7554105	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1001637	chr1:212907611-213034606	Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
2	esv2756884	chr1:212925429-213006397	Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
3	esv2758997	chr1:212925429-213006397	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
4	nsv549149	chr1:212997385-213009657	Enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats	Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	n/a
5	nsv508691	chr1:212998319-213028392	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	n/a
6	nsv549150	chr1:212999701-213011812	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12734406	NSL1	Cis_1M	lymphoblastoid	RTeQTL
rs12734406	LQK1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:212979600-213001000	Weak transcription	Brain Inferior Temporal Lobe	brain
2	chr1:212980800-213001000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr1:212997200-213000200	ZNF genes & repeats	Fetal Intestine Small	intestine
4	chr1:212999400-213009400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr1:212999800-213000400	Weak transcription	HepG2	liver
6	chr1:212999800-213000600	Weak transcription	Stomach Mucosa	stomach
7	chr1:212999800-213003600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr1:212999800-213005000	Weak transcription	Adipose Nuclei	Adipose
9	chr1:212999800-213005000	Weak transcription	Monocytes-CD14+_RO01746	blood

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