Variant report

Variant	rs6467258
Chromosome Location	chr7:80214297-80214298
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 54 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10233710	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10246970	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1093829	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1093830	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1093831	0.89[AFR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1093833	0.89[AFR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1093834	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1093835	0.81[AFR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11764390	0.81[EUR][1000 genomes]
rs1194195	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1194196	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1194197	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12671075	0.86[EUR][1000 genomes]
rs1320408	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1464793	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1608671	0.80[EUR][1000 genomes]
rs1761645	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1761646	0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1761673	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1851934	0.81[ASN][1000 genomes]
rs2177616	0.84[EUR][1000 genomes]
rs2366739	0.82[ASN][1000 genomes]
rs2366744	0.80[EUR][1000 genomes]
rs2781841	0.89[AFR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28851188	0.84[EUR][1000 genomes]
rs28854232	0.84[EUR][1000 genomes]
rs4731606	0.84[EUR][1000 genomes]
rs6467251	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs701269	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs71531176	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs71531177	0.84[EUR][1000 genomes]
rs7779873	0.84[EUR][1000 genomes]
rs7793698	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7794010	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7810280	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs819443	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs819444	0.80[EUR][1000 genomes]
rs819445	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs819455	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs819456	0.93[EUR][1000 genomes]
rs819457	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs819460	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs940542	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9649532	0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv888524	chr7:80107798-80723062	Active TSS Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv831043	chr7:80119414-80322092	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
3	nsv948605	chr7:80119690-80298887	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv1020682	chr7:80120651-80297697	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv888525	chr7:80148668-80232471	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv464606	chr7:80177084-80311794	Active TSS Flanking Active TSS Weak transcription Enhancers Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
7	nsv607682	chr7:80177084-80311794	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
8	nsv1017381	chr7:80187725-80224314	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
9	nsv1025144	chr7:80197286-80271841	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
10	nsv525704	chr7:80203718-80236014	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6467258	ARX	trans	parietal	SCAN
rs6467258	GNAI1	cis	parietal	SCAN
rs6467258	CD36	cis	multi-tissue	Pritchard

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:80209400-80216800	Weak transcription	Primary hematopoietic stem cells	blood
2	chr7:80211000-80223200	Weak transcription	Left Ventricle	heart
3	chr7:80212400-80214800	Enhancers	Fetal Heart	heart
4	chr7:80212600-80226000	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr7:80212800-80214400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr7:80212800-80214400	Enhancers	Osteobl	bone
7	chr7:80212800-80214800	Enhancers	Skeletal Muscle Male	skeletal muscle
8	chr7:80213000-80214400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr7:80213000-80215200	Enhancers	Fetal Intestine Small	intestine
10	chr7:80213200-80214400	Enhancers	NHEK	skin
11	chr7:80213200-80214600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr7:80213200-80214600	Enhancers	HMEC	breast
13	chr7:80213200-80215200	Enhancers	Adipose Nuclei	Adipose
14	chr7:80213600-80223600	Weak transcription	Psoas Muscle	Psoas
15	chr7:80213800-80214400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr7:80213800-80220600	Weak transcription	Fetal Intestine Large	intestine
17	chr7:80214000-80214600	Enhancers	Duodenum Mucosa	Duodenum
18	chr7:80214200-80214400	Enhancers	Pancreas	Pancrea
19	chr7:80214200-80214600	Enhancers	ES-I3 Cell Line	embryonic stem cell
20	chr7:80214200-80214600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr7:80214200-80214600	Enhancers	Primary hematopoietic stem cells short term culture	blood
22	chr7:80214200-80214600	Enhancers	Gastric	stomach
23	chr7:80214200-80214600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
24	chr7:80214200-80214600	Enhancers	Stomach Mucosa	stomach
25	chr7:80214200-80214800	Enhancers	Hela-S3	cervix

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