Variant report

Variant	rs12670579
Chromosome Location	chr7:47868027-47868028
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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

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

rs_ID	r²[population]
rs10245949	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.91[GIH][hapmap];0.94[JPT][hapmap];0.91[MEX][hapmap];0.82[TSI][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13228166	0.81[CHB][hapmap]
rs13237611	0.96[CEU][hapmap]
rs1551275	0.89[CEU][hapmap]
rs17710832	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1980279	1.00[CEU][hapmap];0.91[CHB][hapmap];0.88[GIH][hapmap];0.83[JPT][hapmap];0.82[TSI][hapmap];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2123608	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2177164	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3757379	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3800568	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4543454	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];0.91[MEX][hapmap];0.82[TSI][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6463451	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6947216	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.98[TSI][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6960513	0.92[CEU][hapmap];0.82[CHB][hapmap]
rs6968437	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6975745	0.96[CEU][hapmap]
rs7777539	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7783295	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7783894	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7789224	1.00[CHB][hapmap];0.86[JPT][hapmap];0.88[ASN][1000 genomes]
rs876467	0.92[CEU][hapmap];0.82[CHB][hapmap]
rs9639016	0.96[CEU][hapmap]
rs9639987	0.96[CEU][hapmap]

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	nsv1026223	chr7:47560728-48243287	Genic enhancers Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv888003	chr7:47694270-47907214	Enhancers Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
3	nsv869585	chr7:47765428-48151324	Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
4	nsv830991	chr7:47854530-48025996	Weak transcription Active TSS Genic enhancers Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12670579	SUN3	cis	cerebellum	SCAN

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:47852800-47879000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr7:47855000-47869600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr7:47855000-47880200	Weak transcription	Lung	lung
4	chr7:47855800-47902400	Weak transcription	Adipose Nuclei	Adipose
5	chr7:47859000-47869000	Weak transcription	HSMM	muscle
6	chr7:47865600-47871000	Enhancers	Cortex derived primary cultured neurospheres	brain
7	chr7:47865800-47868200	Enhancers	Fetal Heart	heart
8	chr7:47866200-47868600	Enhancers	Brain Anterior Caudate	brain
9	chr7:47866400-47868400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
10	chr7:47866400-47868400	Enhancers	Fetal Muscle Leg	muscle
11	chr7:47866400-47868600	Enhancers	Pancreas	Pancrea
12	chr7:47866400-47868800	Enhancers	Brain Substantia Nigra	brain
13	chr7:47866400-47869800	Enhancers	HSMMtube	muscle
14	chr7:47866400-47870600	Enhancers	Breast Myoepithelial Primary Cells	Breast
15	chr7:47866600-47868600	Enhancers	Brain Angular Gyrus	brain
16	chr7:47866600-47868600	Enhancers	Brain Inferior Temporal Lobe	brain
17	chr7:47866600-47868600	Enhancers	Fetal Stomach	stomach
18	chr7:47866600-47869800	Enhancers	Brain Cingulate Gyrus	brain
19	chr7:47866800-47868200	Enhancers	Brain Germinal Matrix	brain
20	chr7:47866800-47868200	Enhancers	Left Ventricle	heart
21	chr7:47866800-47868200	Enhancers	Right Ventricle	heart
22	chr7:47866800-47868200	Enhancers	HMEC	breast
23	chr7:47866800-47868400	Enhancers	Fetal Muscle Trunk	muscle
24	chr7:47867200-47868200	Enhancers	Fetal Brain Female	brain
25	chr7:47867200-47871200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr7:47867200-47886000	Weak transcription	Right Atrium	heart
27	chr7:47867400-47868600	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr7:47867400-47869400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr7:47867800-47868400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr7:47867800-47868800	Enhancers	Brain Hippocampus Middle	brain
31	chr7:47867800-47886000	Weak transcription	Skeletal Muscle Male	skeletal muscle
32	chr7:47868000-47868200	Enhancers	Placenta	Placenta

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