Variant report

Variant	rs6943839
Chromosome Location	chr7:26583752-26583753
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:26576661..26579431-chr7:26581573..26583872,2	MCF-7	breast:
2	chr7:26582972..26584768-chr7:26586705..26589472,2	K562	blood:

Variant related genes	Relation type
ENSG00000122548	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10215963	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];0.98[MKK][hapmap];0.98[TSI][hapmap];0.81[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10232686	0.88[EUR][1000 genomes]
rs10232690	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10232785	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10241879	0.81[CEU][hapmap];0.90[CHD][hapmap];0.94[GIH][hapmap];0.88[JPT][hapmap];0.83[TSI][hapmap];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10245341	0.80[CEU][hapmap];0.88[JPT][hapmap];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10262030	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10270966	0.88[JPT][hapmap];0.81[ASN][1000 genomes]
rs1029558	0.85[GIH][hapmap]
rs11982919	0.94[ASN][1000 genomes]
rs2158711	1.00[CHB][hapmap];0.89[JPT][hapmap];0.94[ASN][1000 genomes]
rs2158712	0.86[ASN][1000 genomes]
rs3757655	0.81[CEU][hapmap];0.88[JPT][hapmap];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3757657	0.88[JPT][hapmap];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6953147	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6976270	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6976293	0.83[EUR][1000 genomes]
rs730558	0.85[GIH][hapmap]
rs730955	0.86[CHB][hapmap];0.81[CHD][hapmap];0.84[ASN][1000 genomes]
rs740182	0.82[ASN][1000 genomes]
rs7779755	0.84[ASN][1000 genomes]
rs995993	0.83[ASN][1000 genomes]
rs996550	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1029596	chr7:26302739-26737913	Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
2	nsv538804	chr7:26302739-26737913	Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
3	nsv1025538	chr7:26482342-27376045	Enhancers Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	213 gene(s)	inside rSNPs	diseases
4	nsv538805	chr7:26482342-27376045	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Active TSS Strong transcription Flanking Active TSS Genic enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	213 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6943839	TRA2A	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:26578800-26591600	Enhancers	Primary hematopoietic stem cells short term culture	blood
2	chr7:26579400-26589000	Weak transcription	Fetal Thymus	thymus
3	chr7:26581800-26585200	Enhancers	Fetal Stomach	stomach
4	chr7:26582400-26586800	Enhancers	Fetal Muscle Leg	muscle
5	chr7:26582400-26592200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr7:26582600-26585000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr7:26583000-26584400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr7:26583200-26583800	Flanking Active TSS	Fetal Lung	lung
9	chr7:26583200-26585000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr7:26583400-26583800	Active TSS	Duodenum Smooth Muscle	Duodenum
11	chr7:26583400-26584000	Weak transcription	Primary hematopoietic stem cells	blood
12	chr7:26583400-26586800	Enhancers	Fetal Kidney	kidney
13	chr7:26583600-26584200	Enhancers	Fetal Muscle Trunk	muscle

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