Variant report

Variant	rs7087980
Chromosome Location	chr10:28469074-28469075
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:28030939..28031493-chr10:28468370..28469079,2	MCF-7	breast:
2	chr10:28468637..28470259-chr10:28476879..28479300,2	MCF-7	breast:
3	chr10:28072564..28073290-chr10:28468225..28469172,4	MCF-7	breast:
4	chr10:28153808..28154667-chr10:28468156..28469155,3	MCF-7	breast:
5	chr10:28034470..28035268-chr10:28468503..28469097,2	K562	blood:

Variant related genes	Relation type
ENSG00000251810	Chromatin interaction
ENSG00000150051	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10508734	0.88[TSI][hapmap];0.85[EUR][1000 genomes]
rs10740784	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10826409	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11006908	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.90[MEX][hapmap];0.97[TSI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11598304	1.00[CHD][hapmap]
rs12776665	1.00[CHB][hapmap]
rs17685100	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1781836	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];0.90[MEX][hapmap];0.82[TSI][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1886403	1.00[CHB][hapmap]
rs2124954	1.00[CEU][hapmap];1.00[CHB][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2477345	1.00[CHB][hapmap]
rs2490056	0.81[CEU][hapmap];1.00[CHB][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2490058	1.00[CEU][hapmap];0.87[YRI][hapmap];0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2490060	1.00[CHB][hapmap]
rs2763320	1.00[CHB][hapmap]
rs2800212	1.00[CHB][hapmap]
rs2801839	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2801840	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2985519	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.81[LWK][hapmap];0.95[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2985526	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2985534	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2997201	0.81[CEU][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];0.82[TSI][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2997207	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2997209	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34772309	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4309056	0.88[TSI][hapmap];0.85[EUR][1000 genomes]
rs7894070	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7916791	0.96[CEU][hapmap];1.00[CHB][hapmap];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7919947	0.92[CEU][hapmap];1.00[CHB][hapmap];0.82[GIH][hapmap];0.95[MEX][hapmap];0.87[TSI][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs927675	1.00[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv917149	chr10:28018919-28688694	Enhancers Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv1042524	chr10:28290149-28506812	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
3	nsv831816	chr10:28304698-28493635	Enhancers Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
4	nsv525448	chr10:28337570-28563732	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
5	nsv831817	chr10:28369836-28539930	Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv1041555	chr10:28419399-29304934	Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
7	nsv1037863	chr10:28419399-29378871	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
8	nsv540521	chr10:28419399-29378871	Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7087980	MYO3A	cis	parietal	SCAN
rs7087980	PTCHD3	cis	parietal	SCAN
rs7087980	LOC387646	cis	parietal	SCAN

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:28449800-28497000	Weak transcription	Fetal Intestine Small	intestine
2	chr10:28461400-28469600	Weak transcription	Fetal Heart	heart
3	chr10:28467200-28469800	Enhancers	Fetal Lung	lung
4	chr10:28467200-28470400	Weak transcription	Skeletal Muscle Male	skeletal muscle
5	chr10:28467600-28469600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr10:28467600-28469600	Weak transcription	HSMM	muscle
7	chr10:28467600-28469600	Weak transcription	HSMMtube	muscle
8	chr10:28467600-28470600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr10:28467600-28472600	Weak transcription	Fetal Stomach	stomach
10	chr10:28467600-28485400	Weak transcription	Primary monocytes fromperipheralblood	blood
11	chr10:28467600-28491800	Weak transcription	Psoas Muscle	Psoas
12	chr10:28467600-28525600	Weak transcription	Aorta	Aorta
13	chr10:28467800-28470600	Weak transcription	Osteobl	bone
14	chr10:28467800-28471000	Enhancers	Hela-S3	cervix
15	chr10:28467800-28495200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
16	chr10:28468000-28469400	Weak transcription	Muscle Satellite Cultured Cells	--
17	chr10:28468200-28469200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
18	chr10:28468200-28469600	Weak transcription	Skeletal Muscle Female	skeletal muscle
19	chr10:28468200-28469800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
20	chr10:28468200-28470400	Weak transcription	Colon Smooth Muscle	Colon
21	chr10:28468200-28470600	Weak transcription	Stomach Smooth Muscle	stomach
22	chr10:28468200-28471400	Weak transcription	Rectal Smooth Muscle	rectum
23	chr10:28468200-28484600	Weak transcription	Monocytes-CD14+_RO01746	blood
24	chr10:28468400-28469800	Enhancers	Primary T helper cells PMA-I stimulated	--
25	chr10:28468400-28469800	Enhancers	Primary T helper cells fromperipheralblood	blood
26	chr10:28468400-28470000	Enhancers	Primary T cells from cord blood	blood
27	chr10:28468600-28469200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
28	chr10:28468600-28469600	Weak transcription	Liver	Liver
29	chr10:28468600-28470400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr10:28469000-28469800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
31	chr10:28469000-28471400	Weak transcription	Primary T helper naive cells from peripheral blood	blood

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