Variant report

Variant	rs55936781
Chromosome Location	chr6:166724692-166724693
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	chr6:166722635..166726585-chr6:166755013..166756920,3	K562	blood:
2	chr6:166720530..166722265-chr6:166724559..166726140,2	K562	blood:

Variant related genes	Relation type
ENSG00000176381	Chromatin interaction
ENSG00000198818	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10455809	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10455976	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10455977	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10455978	0.87[EUR][1000 genomes]
rs10946152	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10946154	0.87[ASN][1000 genomes]
rs10946155	0.87[ASN][1000 genomes]
rs10946158	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10946160	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10946161	0.80[EUR][1000 genomes]
rs11752886	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11755305	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12198613	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12209616	0.88[EUR][1000 genomes]
rs12214281	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12214812	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12524268	0.87[ASN][1000 genomes]
rs12526794	0.87[ASN][1000 genomes]
rs12662920	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12662924	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13218257	0.87[ASN][1000 genomes]
rs1599841	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2294333	0.83[EUR][1000 genomes]
rs2294334	0.84[EUR][1000 genomes]
rs2294335	0.84[EUR][1000 genomes]
rs4144886	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4144887	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4144888	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs59337176	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs66461381	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs68016351	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6913024	0.82[ASN][1000 genomes]
rs6913025	0.82[ASN][1000 genomes]
rs6932631	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6935260	0.82[ASN][1000 genomes]
rs6935275	0.82[ASN][1000 genomes]
rs6938819	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs73030701	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs73263155	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs73788236	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7740965	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7753161	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7771603	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9348115	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9348116	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs941683	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9457164	0.87[ASN][1000 genomes]
rs9459648	0.87[ASN][1000 genomes]
rs9459649	0.87[ASN][1000 genomes]
rs9459651	0.86[ASN][1000 genomes]
rs999234	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv886934	chr6:166642850-166747572	Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv886935	chr6:166704744-166726566	Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
3	nsv886936	chr6:166714024-166731289	Active TSS Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs55936781	SFT2D1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:166722600-166732800	Weak transcription	GM12878-XiMat	blood
2	chr6:166722600-166735600	Weak transcription	Brain Angular Gyrus	brain
3	chr6:166722800-166731200	Weak transcription	Spleen	Spleen
4	chr6:166723000-166731400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr6:166723000-166732000	Weak transcription	Gastric	stomach
6	chr6:166723200-166727200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr6:166723200-166732400	Weak transcription	Liver	Liver
8	chr6:166723200-166735400	Weak transcription	Brain Substantia Nigra	brain
9	chr6:166723200-166735600	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr6:166723200-166738800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr6:166723200-166744200	Weak transcription	Right Atrium	heart
12	chr6:166723600-166735800	Weak transcription	Brain Anterior Caudate	brain
13	chr6:166723800-166736000	Weak transcription	Brain Cingulate Gyrus	brain
14	chr6:166724200-166732400	Weak transcription	Primary B cells from peripheral blood	blood

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