Variant report

Variant	rs2451383
Chromosome Location	chr6:34005069-34005070
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:33997116..33999259-chr6:34004517..34006268,2	MCF-7	breast:
2	chr6:34001507..34003993-chr6:34004424..34006060,2	K562	blood:

Extended variants
information (count: 37 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs12111392	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1873250	0.84[CEU][hapmap];0.82[GIH][hapmap];0.84[JPT][hapmap];0.82[TSI][hapmap];0.85[EUR][1000 genomes]
rs2229900	0.91[EUR][1000 genomes]
rs2395554	0.84[EUR][1000 genomes]
rs2451328	0.80[YRI][hapmap]
rs2451358	0.84[EUR][1000 genomes]
rs2451361	0.85[YRI][hapmap]
rs2451378	0.83[AMR][1000 genomes]
rs2451379	0.87[AMR][1000 genomes]
rs2451381	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2451382	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2451384	0.94[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2451385	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2451386	0.96[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2451387	0.94[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2499672	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2499673	1.00[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2499674	1.00[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2499675	1.00[CEU][hapmap];0.95[CHB][hapmap];0.88[JPT][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2499676	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2499677	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];0.84[JPT][hapmap];0.90[LWK][hapmap];0.89[MEX][hapmap];0.97[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3103432	0.96[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34208448	0.80[EUR][1000 genomes]
rs34906910	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35075443	0.95[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35411382	0.95[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3778050	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3798529	0.96[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4713736	0.84[EUR][1000 genomes]
rs71556962	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9394185	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[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	nsv916210	chr6:33804111-34144062	Weak transcription Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA	32 gene(s)	inside rSNPs	diseases
2	nsv462900	chr6:33932442-34195011	Bivalent/Poised TSS Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	17 gene(s)	inside rSNPs	diseases
3	nsv602843	chr6:33932442-34195011	Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Weak transcription ZNF genes & repeats Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	17 gene(s)	inside rSNPs	diseases
4	nsv885778	chr6:33942228-34007054	Bivalent Enhancer Active TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	4 gene(s)	inside rSNPs	diseases
5	nsv462901	chr6:33953646-34050917	ZNF genes & repeats Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
6	nsv602861	chr6:33953646-34050917	Weak transcription Bivalent Enhancer Enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2451383	TMEM217	cis	parietal	SCAN
rs2451383	NUDT3	cis	parietal	SCAN
rs2451383	GRM4	cis	cerebellum	SCAN

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:33984000-34010200	Weak transcription	Brain Anterior Caudate	brain
2	chr6:33984400-34023000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr6:33986200-34009600	Weak transcription	Right Atrium	heart
4	chr6:33988000-34013600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr6:33994400-34013000	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr6:34000200-34016000	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr6:34002800-34027000	Weak transcription	Spleen	Spleen
8	chr6:34003800-34006600	Enhancers	GM12878-XiMat	blood
9	chr6:34004000-34013400	Weak transcription	HUES48 Cell Line	embryonic stem cell
10	chr6:34004200-34013400	Weak transcription	HUES6 Cell Line	embryonic stem cell
11	chr6:34004400-34008600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr6:34004400-34011000	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr6:34004400-34013400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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