Variant report

Variant	rs3789228
Chromosome Location	chr6:24287551-24287552
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	chr6:24284969..24286871-chr6:24287249..24289411,2	K562	blood:
2	chr6:24284945..24286564-chr6:24287420..24288953,2	MCF-7	breast:

Extended variants
information (count: 25 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10806986	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10946689	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11754080	0.88[JPT][hapmap]
rs12055879	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12197973	0.84[ASN][1000 genomes]
rs12216513	0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1578349	0.93[ASN][1000 genomes]
rs2274305	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2296539	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2328208	0.81[ASN][1000 genomes]
rs4712817	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6456601	0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs793843	0.80[EUR][1000 genomes]
rs807697	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs807698	0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs807700	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs807701	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs807722	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs870601	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9295620	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9379649	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9379650	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9393541	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1029930	chr6:23481989-24289948	Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv427746	chr6:24221299-24305709	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs3789228	GMNN	cis	cerebellum	SCAN
rs3789228	HIST1H4A	cis	parietal	SCAN
rs3789228	DCDC2	cis	parietal	SCAN
rs3789228	PRSS16	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:24284000-24288400	Weak transcription	Spleen	Spleen
2	chr6:24284200-24292000	Weak transcription	Fetal Intestine Large	intestine
3	chr6:24284200-24294200	Weak transcription	Fetal Intestine Small	intestine
4	chr6:24284600-24292000	Weak transcription	A549	lung
5	chr6:24284600-24302800	Weak transcription	Pancreas	Pancrea
6	chr6:24285000-24287800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr6:24286600-24287800	Strong transcription	Fetal Kidney	kidney
8	chr6:24286800-24288200	Genic enhancers	HepG2	liver
9	chr6:24287000-24288000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain

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