Variant report

Variant	rs227840
Chromosome Location	chr6:44686304-44686305
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:44681475..44683976-chr6:44685935..44688011,2	K562	blood:
2	chr6:44684410..44686836-chr6:44696222..44698062,2	MCF-7	breast:

Extended variants
information (count: 52 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs12192367	0.83[JPT][hapmap]
rs12529522	1.00[ASW][hapmap];0.88[CHB][hapmap]
rs12530016	0.88[CHB][hapmap]
rs13206206	0.99[ASN][1000 genomes]
rs13206526	0.94[CHB][hapmap];0.90[MEX][hapmap]
rs1402599	0.94[CHB][hapmap]
rs1418435	0.87[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs16869119	1.00[CHB][hapmap]
rs1935549	0.80[AMR][1000 genomes]
rs2139863	1.00[CHB][hapmap]
rs227827	0.84[ASN][1000 genomes]
rs227830	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs227832	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs227833	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs227835	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs227836	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs227839	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs227844	0.96[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	0.89[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs227853	0.89[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs227854	0.82[EUR][1000 genomes]
rs227857	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34577161	0.87[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs35376827	0.99[ASN][1000 genomes]
rs3799965	1.00[CHB][hapmap];0.90[MEX][hapmap]
rs3799968	0.86[CHD][hapmap]
rs3799972	1.00[CHB][hapmap]
rs3799974	1.00[CHB][hapmap]
rs3823252	1.00[CHB][hapmap];0.90[MEX][hapmap]
rs3997503	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4711797	0.88[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs4714812	1.00[ASW][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.90[MEX][hapmap];0.81[TSI][hapmap];0.87[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs4714813	0.82[EUR][1000 genomes]
rs4714825	0.80[AMR][1000 genomes]
rs524492	0.94[CHB][hapmap]
rs542444	1.00[CHB][hapmap];0.95[MEX][hapmap];0.81[TSI][hapmap];0.81[AMR][1000 genomes]
rs609643	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs609699	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs687878	0.82[EUR][1000 genomes]
rs72664272	0.90[AMR][1000 genomes]
rs7746032	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7769218	1.00[CHB][hapmap]
rs9369514	0.84[CHD][hapmap]
rs9463017	0.87[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs9463039	0.85[AMR][1000 genomes]
rs9463040	0.85[AMR][1000 genomes]
rs9472331	1.00[CHB][hapmap];0.94[JPT][hapmap];0.87[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs9472335	0.87[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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs227840	SUPT3H	cis	multi-tissue	Pritchard
rs227840	CUL7	cis	cerebellum	SCAN
rs227840	SUPT3H	cis	lymphoblastoid	seeQTL

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:44667200-44691000	Weak transcription	Right Atrium	heart
2	chr6:44682400-44691000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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