Variant report

Variant	rs6961824
Chromosome Location	chr7:80167067-80167068
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 47 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10215822	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10215825	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10229705	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10239813	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10249397	0.89[EUR][1000 genomes]
rs10265053	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10278120	0.89[EUR][1000 genomes]
rs12531594	0.93[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs12669206	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12706865	0.82[EUR][1000 genomes]
rs13222156	0.93[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs13222395	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13237390	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13242267	0.90[EUR][1000 genomes]
rs13245374	0.93[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs1464794	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1524601	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1851937	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1931693	0.90[EUR][1000 genomes]
rs1965524	0.90[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs1965525	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2091178	0.89[EUR][1000 genomes]
rs2091180	0.88[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs2210684	0.90[EUR][1000 genomes]
rs2366741	0.93[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs28782219	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28850277	0.93[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs28872565	0.90[EUR][1000 genomes]
rs35136290	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4728156	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4728157	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs59057809	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62459940	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6467245	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6944746	0.90[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs6945398	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7778094	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7797266	0.89[AFR][1000 genomes];0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv429785	chr7:79589749-80177049	Bivalent/Poised TSS Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv1030961	chr7:80032525-80197468	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	nsv538991	chr7:80032525-80197468	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv949205	chr7:80039695-80211200	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	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
6	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
7	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
8	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
9	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6961824	ARX	trans	parietal	SCAN

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:80159000-80171400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
2	chr7:80163200-80167200	Weak transcription	HMEC	breast
3	chr7:80163200-80167600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr7:80163200-80167600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr7:80165600-80168000	Enhancers	Primary monocytes fromperipheralblood	blood
6	chr7:80165600-80168400	Enhancers	Primary hematopoietic stem cells short term culture	blood
7	chr7:80166000-80168000	Enhancers	Monocytes-CD14+_RO01746	blood
8	chr7:80166200-80168200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr7:80166400-80168000	Enhancers	Adipose Nuclei	Adipose
10	chr7:80166400-80168200	Enhancers	Primary neutrophils fromperipheralblood	blood
11	chr7:80166600-80167600	Weak transcription	Fetal Muscle Leg	muscle
12	chr7:80166600-80168000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr7:80166600-80168000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr7:80166600-80168400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr7:80166800-80167200	Enhancers	A549	lung
16	chr7:80167000-80167600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr7:80167000-80168200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr7:80167000-80168200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin

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