Variant report

Variant	rs10055039
Chromosome Location	chr5:115490065-115490066
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:115473230..115475072-chr5:115489118..115491844,2	MCF-7	breast:

Extended variants
information (count: 105 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:85)

rs_ID	r²[population]
rs10040031	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10042163	1.00[ASW][hapmap];1.00[LWK][hapmap];0.93[MEX][hapmap];0.83[MKK][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes]
rs10045890	0.87[ASN][1000 genomes]
rs10051539	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10054121	0.85[CHB][hapmap];0.85[CHD][hapmap]
rs10057577	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10058954	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10060732	0.83[ASN][1000 genomes]
rs10072350	0.82[ASN][1000 genomes]
rs10072373	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10072417	0.82[ASN][1000 genomes]
rs10072430	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10075082	0.92[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.90[EUR][1000 genomes]
rs10478283	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10900713	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11241361	0.87[ASN][1000 genomes]
rs11241362	0.87[ASN][1000 genomes]
rs11241363	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1133186	0.85[CHB][hapmap];0.90[CHD][hapmap]
rs11738779	0.83[ASN][1000 genomes]
rs11742121	0.82[ASN][1000 genomes]
rs11957456	1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs12055304	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12653124	0.82[YRI][hapmap]
rs13190092	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1396480	1.00[YRI][hapmap];0.84[AFR][1000 genomes]
rs1396497	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs1508874	1.00[ASW][hapmap];1.00[LWK][hapmap];0.93[MEX][hapmap];0.83[MKK][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes]
rs1508884	1.00[ASW][hapmap];0.87[LWK][hapmap];0.85[MEX][hapmap];1.00[YRI][hapmap]
rs153614	1.00[YRI][hapmap]
rs1588268	0.83[ASN][1000 genomes]
rs168833	1.00[YRI][hapmap]
rs194182	0.82[YRI][hapmap]
rs2063252	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2136206	1.00[YRI][hapmap];0.97[AFR][1000 genomes]
rs2136211	0.89[EUR][1000 genomes]
rs2136212	1.00[YRI][hapmap]
rs2202816	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2416425	0.82[ASN][1000 genomes]
rs2416429	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2416431	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs253960	0.82[YRI][hapmap]
rs28125	0.82[YRI][hapmap]
rs37182	0.82[YRI][hapmap]
rs3933997	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4463206	1.00[YRI][hapmap];0.84[AFR][1000 genomes]
rs4920904	0.85[CHB][hapmap]
rs4920905	1.00[CHB][hapmap];0.95[CHD][hapmap];0.92[GIH][hapmap];0.91[JPT][hapmap];0.86[MEX][hapmap]
rs4920906	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4921056	0.85[CHB][hapmap];0.82[JPT][hapmap]
rs4921057	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs4921061	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4921064	0.87[ASN][1000 genomes]
rs4921066	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6594942	0.88[ASN][1000 genomes]
rs6594943	0.81[ASN][1000 genomes]
rs6594946	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6594947	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6594950	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6594953	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6594954	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6594955	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6860795	1.00[YRI][hapmap];0.92[AFR][1000 genomes]
rs6863734	1.00[CHB][hapmap];0.88[CHD][hapmap];0.89[GIH][hapmap];0.82[JPT][hapmap];0.96[TSI][hapmap];0.87[EUR][1000 genomes]
rs6872757	0.82[ASN][1000 genomes]
rs6877029	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6878279	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs6881750	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6896119	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6896147	1.00[CHB][hapmap];0.95[CHD][hapmap];0.92[GIH][hapmap];0.91[JPT][hapmap];0.86[MEX][hapmap]
rs6896229	1.00[ASW][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs6896571	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7701512	1.00[YRI][hapmap]
rs7704903	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.93[MEX][hapmap];0.96[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7722829	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7726721	0.92[AFR][1000 genomes]
rs7733992	1.00[ASW][hapmap];1.00[LWK][hapmap];0.93[MEX][hapmap];1.00[YRI][hapmap]
rs7734133	0.95[CHB][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs784482	1.00[ASW][hapmap];0.93[LWK][hapmap];0.86[MEX][hapmap];0.83[MKK][hapmap];0.82[YRI][hapmap]
rs804141	1.00[YRI][hapmap]
rs9285884	1.00[YRI][hapmap];0.89[AFR][1000 genomes]
rs9326985	1.00[ASW][hapmap];1.00[LWK][hapmap];0.93[MEX][hapmap];1.00[YRI][hapmap]
rs9326992	1.00[ASW][hapmap];1.00[LWK][hapmap];0.83[MKK][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes]
rs9326993	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9687859	1.00[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:20 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949677	chr5:115104829-115496168	Enhancers Weak transcription Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv882736	chr5:115254723-115552945	Weak transcription Bivalent/Poised TSS Bivalent Enhancer Enhancers Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
3	nsv882737	chr5:115263853-115552945	Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
4	esv34146	chr5:115315944-115729919	Flanking Active TSS Enhancers ZNF genes & repeats Weak transcription Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
5	nsv527320	chr5:115382097-115573543	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
6	nsv1027266	chr5:115382704-115501792	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
7	esv2755349	chr5:115384101-115733101	Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
8	nsv1032199	chr5:115384131-115525738	Enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
9	esv2830404	chr5:115386661-115490546	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
10	nsv1019972	chr5:115386860-115563533	Flanking Active TSS Enhancers Active TSS Strong transcription Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
11	nsv537869	chr5:115386860-115563533	Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
12	nsv1018861	chr5:115397834-115563533	Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
13	nsv537870	chr5:115397834-115563533	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
14	nsv882739	chr5:115471015-115552945	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
15	nsv1016891	chr5:115477740-115523778	Strong transcription ZNF genes & repeats Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
16	nsv537871	chr5:115477740-115523778	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
17	nsv882740	chr5:115482794-115540041	Weak transcription ZNF genes & repeats Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
18	nsv882741	chr5:115484252-115552945	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
19	nsv1032531	chr5:115489694-115583800	Enhancers ZNF genes & repeats Weak transcription Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
20	nsv882742	chr5:115489770-115584159	ZNF genes & repeats Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10055039	ATG12	cis	cerebellum	SCAN

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:115462600-115502000	Weak transcription	Fetal Intestine Large	intestine
2	chr5:115468200-115494400	Weak transcription	Primary T cells from cord blood	blood
3	chr5:115468600-115501400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
4	chr5:115471600-115521600	Weak transcription	Primary B cells from peripheral blood	blood
5	chr5:115472800-115500200	Weak transcription	Primary B cells from cord blood	blood
6	chr5:115472800-115500400	Weak transcription	Monocytes-CD14+_RO01746	blood
7	chr5:115473600-115494800	Weak transcription	Fetal Kidney	kidney
8	chr5:115473600-115495200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
9	chr5:115481400-115536000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
10	chr5:115484400-115510000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr5:115484400-115521400	Weak transcription	Primary T helper cells fromperipheralblood	blood
12	chr5:115488400-115501200	Weak transcription	Psoas Muscle	Psoas
13	chr5:115489200-115490800	Enhancers	HepG2	liver
14	chr5:115489200-115491000	Enhancers	Liver	Liver
15	chr5:115489200-115526800	Weak transcription	Pancreas	Pancrea
16	chr5:115489800-115494600	Weak transcription	Fetal Heart	heart
17	chr5:115489800-115528600	Weak transcription	Ovary	ovary
18	chr5:115490000-115491000	Enhancers	Pancreatic Islets	Pancreatic Islet
19	chr5:115490000-115524400	Weak transcription	Left Ventricle	heart

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