Variant report

Variant	rs6692318
Chromosome Location	chr1:67134326-67134327
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	STAT3	chr1:67134181-67134381	MCF10A-Er-Src	breast:	n/a	n/a

Variant related genes	Relation type
SGIP1	TF binding region

Extended variants
information (count: 42 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10493412	1.00[ASW][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs10493413	1.00[CHB][hapmap];1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10889630	0.86[CHB][hapmap];0.86[JPT][hapmap];0.88[YRI][hapmap]
rs10889645	0.85[JPT][hapmap]
rs10889646	0.82[JPT][hapmap]
rs11208921	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs11208933	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs11208935	0.85[ASN][1000 genomes]
rs11208943	0.86[JPT][hapmap]
rs11208946	0.86[JPT][hapmap]
rs1159632	0.86[CHB][hapmap];0.86[JPT][hapmap]
rs12077192	0.85[ASN][1000 genomes]
rs12117202	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs12137531	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[ASN][1000 genomes]
rs12141816	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs12407460	1.00[ASW][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1325262	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[ASN][1000 genomes]
rs1325264	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1536112	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs17129256	0.85[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs17129302	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs17129310	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17129313	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17129315	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17129318	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17436311	1.00[ASW][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs1998716	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs2025594	0.86[JPT][hapmap]
rs2147776	0.85[ASN][1000 genomes]
rs4147266	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap]
rs45467391	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs56004227	0.87[ASN][1000 genomes]
rs56374735	0.85[ASN][1000 genomes]
rs6687096	0.86[CHB][hapmap];0.86[JPT][hapmap]
rs6689755	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs6699200	0.86[CHB][hapmap];0.86[JPT][hapmap];0.87[YRI][hapmap]
rs6703606	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs72669476	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs72669484	0.97[AFR][1000 genomes];0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs7548488	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[ASN][1000 genomes]
rs975878	0.85[CHB][hapmap];0.85[JPT][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869413	chr1:67082512-67414286	Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6692318	ATG4C	cis	parietal	SCAN

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:67090400-67155000	Weak transcription	Fetal Heart	heart
2	chr1:67100000-67144400	Weak transcription	Left Ventricle	heart
3	chr1:67106200-67143000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
4	chr1:67108000-67136200	Weak transcription	Fetal Brain Female	brain
5	chr1:67109200-67141800	Weak transcription	Muscle Satellite Cultured Cells	--
6	chr1:67109600-67155000	Weak transcription	Brain Anterior Caudate	brain
7	chr1:67110800-67134400	Weak transcription	Brain Substantia Nigra	brain
8	chr1:67111000-67135200	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr1:67111400-67154800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr1:67114200-67142000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr1:67114200-67156400	Weak transcription	Stomach Smooth Muscle	stomach
12	chr1:67114600-67142200	Weak transcription	NHLF	lung
13	chr1:67118800-67138800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr1:67118800-67140400	Weak transcription	Aorta	Aorta
15	chr1:67121200-67145400	Weak transcription	Brain Angular Gyrus	brain
16	chr1:67122000-67141200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr1:67126600-67134800	Weak transcription	Fetal Kidney	kidney
18	chr1:67131800-67141600	Weak transcription	NH-A	brain
19	chr1:67133200-67139200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr1:67133200-67141800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr1:67134000-67136000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr1:67134200-67135000	Enhancers	Brain Cingulate Gyrus	brain
23	chr1:67134200-67135200	Enhancers	Brain Hippocampus Middle	brain

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