Variant report

Variant	rs7712778
Chromosome Location	chr5:42694307-42694308
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 28 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10512806	0.82[ASN][1000 genomes]
rs10805665	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs10941590	1.00[JPT][hapmap]
rs11749941	0.82[ASN][1000 genomes]
rs13153784	1.00[JPT][hapmap]
rs13154178	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs35291899	0.91[EUR][1000 genomes]
rs4146624	1.00[CEU][hapmap]
rs57062650	0.82[ASN][1000 genomes]
rs60268063	0.82[ASN][1000 genomes]
rs6176	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6875431	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6886900	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6889182	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6889614	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72552397	1.00[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7730819	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv933208	chr5:41879946-42876624	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	112 gene(s)	inside rSNPs	diseases
2	nsv492147	chr5:41902086-42896162	Enhancers Flanking Active TSS Active TSS Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	113 gene(s)	inside rSNPs	diseases
3	nsv1020464	chr5:42488628-42699394	Active TSS Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv1018751	chr5:42491883-42697923	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv1031160	chr5:42610090-42843255	Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
6	nsv1019696	chr5:42610090-42844191	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
7	nsv597886	chr5:42610409-42854408	Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
8	nsv1029933	chr5:42611976-42833385	Enhancers Transcr. at gene 5' and 3' Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
9	nsv537735	chr5:42611976-42833385	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
10	nsv1019648	chr5:42616487-42696943	Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
11	nsv537736	chr5:42616487-42696943	Strong transcription Genic enhancers Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7712778	C6orf48	trans	lymphoblastoid	seeQTL

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:42687800-42700600	Weak transcription	Fetal Intestine Large	intestine
2	chr5:42688000-42699800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
3	chr5:42688400-42722200	Weak transcription	Pancreas	Pancrea
4	chr5:42688600-42699000	Weak transcription	Esophagus	oesophagus
5	chr5:42689800-42703000	Strong transcription	Liver	Liver
6	chr5:42689800-42703400	Strong transcription	Adipose Nuclei	Adipose
7	chr5:42690400-42700000	Weak transcription	Fetal Muscle Trunk	muscle
8	chr5:42690400-42701200	Weak transcription	Fetal Lung	lung
9	chr5:42692000-42694600	Weak transcription	Brain Angular Gyrus	brain
10	chr5:42692200-42696800	Weak transcription	Stomach Smooth Muscle	stomach
11	chr5:42692200-42697400	Weak transcription	Left Ventricle	heart
12	chr5:42692200-42697400	Weak transcription	Ovary	ovary
13	chr5:42692200-42700800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr5:42692200-42703000	Weak transcription	Rectal Smooth Muscle	rectum
15	chr5:42692200-42703200	Weak transcription	Duodenum Smooth Muscle	Duodenum
16	chr5:42692200-42703200	Weak transcription	Right Ventricle	heart
17	chr5:42692200-42705600	Weak transcription	Fetal Muscle Leg	muscle
18	chr5:42692400-42705600	Weak transcription	Colon Smooth Muscle	Colon
19	chr5:42692600-42697400	Weak transcription	Fetal Stomach	stomach
20	chr5:42692600-42698000	Weak transcription	Fetal Heart	heart
21	chr5:42692600-42702800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr5:42693000-42699000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
23	chr5:42693600-42694600	Strong transcription	Skeletal Muscle Male	skeletal muscle
24	chr5:42693800-42695400	Strong transcription	Skeletal Muscle Female	skeletal muscle
25	chr5:42694000-42695800	Weak transcription	Spleen	Spleen
26	chr5:42694000-42696200	Weak transcription	Aorta	Aorta
27	chr5:42694000-42697800	Weak transcription	Psoas Muscle	Psoas

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