Variant report

Variant	rs1980279
Chromosome Location	chr7:47884829-47884830
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:47879370..47881092-chr7:47882304..47884978,2	MCF-7	breast:
2	chr7:47884198..47887290-chr7:48007408..48010423,4	MCF-7	breast:

Extended variants
information (count: 28 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10245949	1.00[CEU][hapmap];0.91[CHB][hapmap];0.89[CHD][hapmap];0.98[GIH][hapmap];0.89[JPT][hapmap];0.86[MEX][hapmap];0.89[MKK][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12670579	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]
rs13228166	0.89[CHB][hapmap]
rs13237611	0.96[CEU][hapmap];0.82[CHB][hapmap];0.87[CHD][hapmap];0.91[MEX][hapmap];0.89[TSI][hapmap];0.86[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs1551275	0.89[CEU][hapmap];0.82[CHB][hapmap];0.86[CHD][hapmap];0.85[TSI][hapmap];0.83[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs17710832	1.00[CEU][hapmap];0.91[CHB][hapmap];0.83[JPT][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2123608	1.00[CEU][hapmap];0.90[CHB][hapmap];0.82[JPT][hapmap];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2177164	1.00[CEU][hapmap];0.91[CHB][hapmap];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3757379	1.00[CEU][hapmap];0.90[CHB][hapmap];0.83[JPT][hapmap];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3800568	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];0.85[ASN][1000 genomes]
rs4543454	1.00[CEU][hapmap];0.91[CHB][hapmap];0.89[CHD][hapmap];0.93[GIH][hapmap];0.89[JPT][hapmap];0.86[MEX][hapmap];0.95[TSI][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6463451	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6947216	1.00[CEU][hapmap];0.91[CHB][hapmap];0.88[GIH][hapmap];0.83[JPT][hapmap];0.80[TSI][hapmap];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6960513	0.92[CEU][hapmap];0.84[AMR][1000 genomes]
rs6968437	1.00[CEU][hapmap];0.90[CHB][hapmap];0.86[JPT][hapmap];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6975745	0.96[CEU][hapmap];0.81[CHB][hapmap];0.90[AMR][1000 genomes];0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7777539	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7783295	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]
rs7783894	1.00[CEU][hapmap];0.90[CHB][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7789224	0.89[CHB][hapmap]
rs876467	0.92[CEU][hapmap];0.89[TSI][hapmap];0.81[AMR][1000 genomes]
rs9639016	0.96[CEU][hapmap];0.82[CHB][hapmap];0.90[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs9639987	0.96[CEU][hapmap];0.82[CHB][hapmap];0.90[MEX][hapmap];0.89[TSI][hapmap];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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
5	nsv532120	chr7:47882757-48195869	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1980279	SUN3	cis	cerebellum	SCAN
rs1980279	VWC2	cis	cerebellum	SCAN

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:47855800-47902400	Weak transcription	Adipose Nuclei	Adipose
2	chr7:47867200-47886000	Weak transcription	Right Atrium	heart
3	chr7:47867800-47886000	Weak transcription	Skeletal Muscle Male	skeletal muscle
4	chr7:47868800-47886000	Weak transcription	Skeletal Muscle Female	skeletal muscle
5	chr7:47869800-47885400	Weak transcription	HSMMtube	muscle
6	chr7:47882600-47886000	Weak transcription	Gastric	stomach
7	chr7:47883200-47886000	Enhancers	Hela-S3	cervix
8	chr7:47883400-47885800	Enhancers	Fetal Heart	heart
9	chr7:47883600-47885800	Enhancers	A549	lung
10	chr7:47884400-47887200	Enhancers	HUVEC	blood vessel
11	chr7:47884600-47885400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr7:47884800-47885000	Bivalent Enhancer	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr7:47884800-47885000	Genic enhancers	Right Ventricle	heart
14	chr7:47884800-47885400	Enhancers	Left Ventricle	heart
15	chr7:47884800-47886000	Weak transcription	Lung	lung
16	chr7:47884800-47886400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr7:47884800-47887000	Enhancers	HSMM	muscle

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