Variant report

Variant	rs12055879
Chromosome Location	chr6:24274117-24274118
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:24273970..24276179-chr6:24277278..24279820,2	MCF-7	breast:

Extended variants
information (count: 26 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10806986	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10946689	0.91[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11754080	0.94[JPT][hapmap]
rs12197973	0.87[ASN][1000 genomes]
rs12216513	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1578349	0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2274305	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2296539	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3789228	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3846832	0.80[AFR][1000 genomes]
rs4712817	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4712818	0.80[AFR][1000 genomes]
rs6456601	0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs793843	0.87[EUR][1000 genomes]
rs807697	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs807698	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs807700	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs807701	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs807722	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs870601	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9295620	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9379649	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9379650	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9393541	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[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
rs12055879	GMNN	cis	cerebellum	SCAN
rs12055879	HIST1H4A	cis	parietal	SCAN
rs12055879	DCDC2	cis	parietal	SCAN
rs12055879	PRSS16	cis	parietal	SCAN

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:24263000-24283000	Weak transcription	Fetal Intestine Large	intestine
2	chr6:24270200-24274800	Strong transcription	HepG2	liver
3	chr6:24270400-24283800	Weak transcription	Pancreas	Pancrea
4	chr6:24271200-24283400	Weak transcription	Fetal Intestine Small	intestine
5	chr6:24273000-24274400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr6:24273000-24274400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
7	chr6:24273400-24274200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr6:24273600-24274600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr6:24273800-24274400	Enhancers	Skeletal Muscle Male	skeletal muscle
10	chr6:24273800-24274600	Enhancers	Fetal Kidney	kidney
11	chr6:24273800-24274800	Enhancers	Brain Germinal Matrix	brain
12	chr6:24273800-24274800	Enhancers	Colon Smooth Muscle	Colon
13	chr6:24274000-24274200	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr6:24274000-24274200	Enhancers	HSMM	muscle
15	chr6:24274000-24274400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin

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