Variant report

Variant	rs227832
Chromosome Location	chr6:44681257-44681258
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	chr6:44681103..44683539-chr6:44690355..44693257,2	MCF-7	breast:

Extended variants
information (count: 55 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs12192367	0.83[JPT][hapmap]
rs12529132	0.90[AFR][1000 genomes]
rs12529522	0.88[CHB][hapmap]
rs12530016	0.88[CHB][hapmap]
rs13206206	0.99[ASN][1000 genomes]
rs13206526	0.94[CHB][hapmap];0.86[MEX][hapmap]
rs1402599	0.94[CHB][hapmap]
rs1418435	0.83[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs16869119	1.00[CHB][hapmap]
rs2139863	1.00[CHB][hapmap]
rs227820	0.84[AFR][1000 genomes]
rs227822	0.82[AFR][1000 genomes]
rs227823	0.82[AFR][1000 genomes]
rs227827	0.84[ASN][1000 genomes]
rs227830	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs227833	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs227835	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs227836	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs227839	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs227840	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs227844	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs227845	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs227849	0.87[CHD][hapmap];0.83[JPT][hapmap]
rs227852	0.86[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.90[TSI][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs227853	0.95[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.90[TSI][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs227854	0.82[EUR][1000 genomes]
rs227857	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34577161	0.83[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs35376827	0.99[ASN][1000 genomes]
rs3799965	1.00[CHB][hapmap];0.86[MEX][hapmap]
rs3799968	0.86[CHD][hapmap]
rs3799972	1.00[CHB][hapmap]
rs3799974	1.00[CHB][hapmap]
rs3823252	1.00[CHB][hapmap];0.86[MEX][hapmap]
rs3997503	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4711797	0.84[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs4714812	1.00[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.86[MEX][hapmap];0.83[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs4714813	0.81[EUR][1000 genomes]
rs524492	0.94[CHB][hapmap]
rs542444	1.00[CHB][hapmap];0.91[MEX][hapmap]
rs609643	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs609699	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs679769	0.85[AFR][1000 genomes]
rs687878	0.82[EUR][1000 genomes]
rs72664272	0.85[AMR][1000 genomes]
rs7746032	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7769218	1.00[CHB][hapmap]
rs9369514	0.84[CHD][hapmap]
rs9463017	0.83[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs9463039	0.81[AMR][1000 genomes]
rs9463040	0.81[AMR][1000 genomes]
rs9472331	1.00[CHB][hapmap];0.94[JPT][hapmap];0.83[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs9472335	0.83[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs9472376	0.94[CHB][hapmap]

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	esv1817071	chr6:44670110-44698829	Enhancers Bivalent Enhancer Weak transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs227832	TCTE1	cis	parietal	SCAN
rs227832	SLC22A7	cis	cerebellum	SCAN
rs227832	CUL7	cis	cerebellum	SCAN
rs227832	SUPT3H	cis	lymphoblastoid	seeQTL
rs227832	SLC25A27	cis	parietal	SCAN
rs227832	SPATS1	cis	cerebellum	SCAN
rs227832	SUPT3H	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:44667200-44691000	Weak transcription	Right Atrium	heart
2	chr6:44679400-44683600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr6:44679600-44681600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr6:44679600-44682400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr6:44679800-44682200	Enhancers	Fetal Muscle Leg	muscle
6	chr6:44680000-44681400	Enhancers	HSMMtube	muscle
7	chr6:44680200-44681400	Enhancers	HSMM	muscle
8	chr6:44680600-44681400	Enhancers	Fetal Intestine Large	intestine
9	chr6:44680800-44682200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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