Variant report

Variant	rs2415120
Chromosome Location	chr15:72105544-72105545
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:72097461..72102477-chr15:72104726..72109263,4	MCF-7	breast:
2	chr15:71265292..71267495-chr15:72104679..72106559,2	MCF-7	breast:

Extended variants
information (count: 79 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs1074330	0.83[CEU][hapmap]
rs10851847	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11633167	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs11634608	1.00[CEU][hapmap];0.89[GIH][hapmap];0.84[JPT][hapmap];0.89[TSI][hapmap];0.87[EUR][1000 genomes]
rs12050794	0.91[EUR][1000 genomes]
rs12148078	0.82[EUR][1000 genomes]
rs12439494	0.94[CEU][hapmap];0.87[EUR][1000 genomes]
rs12898728	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12898868	0.86[AFR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12902006	0.83[CEU][hapmap]
rs12912771	0.87[EUR][1000 genomes]
rs12916951	0.83[CEU][hapmap]
rs1481862	0.86[EUR][1000 genomes]
rs16956273	0.89[CEU][hapmap];0.87[GIH][hapmap];0.82[TSI][hapmap]
rs16956369	0.91[EUR][1000 genomes]
rs2128112	0.91[EUR][1000 genomes]
rs2306489	0.82[EUR][1000 genomes]
rs2306576	1.00[CEU][hapmap];0.89[GIH][hapmap];0.87[MEX][hapmap];0.92[TSI][hapmap];0.93[EUR][1000 genomes]
rs2415121	0.90[EUR][1000 genomes]
rs2415126	0.93[EUR][1000 genomes]
rs2415128	0.94[CEU][hapmap];0.89[GIH][hapmap];0.81[MEX][hapmap];0.90[TSI][hapmap];0.89[EUR][1000 genomes]
rs28650442	0.90[EUR][1000 genomes]
rs28717020	0.88[EUR][1000 genomes]
rs2899775	0.84[EUR][1000 genomes]
rs2899776	0.87[EUR][1000 genomes]
rs2929508	0.93[CEU][hapmap];0.86[EUR][1000 genomes]
rs2929509	0.87[EUR][1000 genomes]
rs2929510	0.86[EUR][1000 genomes]
rs2929511	0.87[EUR][1000 genomes]
rs2929513	0.86[EUR][1000 genomes]
rs2929517	0.85[EUR][1000 genomes]
rs2929525	0.81[EUR][1000 genomes]
rs2929526	0.82[EUR][1000 genomes]
rs2929527	0.84[EUR][1000 genomes]
rs2929532	0.85[EUR][1000 genomes]
rs2930069	0.86[EUR][1000 genomes]
rs2957361	0.85[EUR][1000 genomes]
rs2957365	0.84[EUR][1000 genomes]
rs2957724	1.00[CEU][hapmap];0.81[YRI][hapmap];0.85[EUR][1000 genomes]
rs2957725	0.94[CEU][hapmap];0.84[GIH][hapmap];0.81[MEX][hapmap];0.84[TSI][hapmap]
rs2957728	0.86[EUR][1000 genomes]
rs2957734	1.00[CEU][hapmap];0.89[GIH][hapmap];0.88[MEX][hapmap];0.92[TSI][hapmap];0.87[EUR][1000 genomes]
rs2957735	1.00[CEU][hapmap];0.89[GIH][hapmap];0.87[MEX][hapmap];0.92[TSI][hapmap];0.86[EUR][1000 genomes]
rs2957736	0.86[EUR][1000 genomes]
rs2957737	0.94[CEU][hapmap];0.81[GIH][hapmap];0.81[MEX][hapmap];0.84[TSI][hapmap]
rs2957740	0.86[EUR][1000 genomes]
rs2957742	0.86[EUR][1000 genomes]
rs2957745	0.85[EUR][1000 genomes]
rs2957746	0.81[EUR][1000 genomes]
rs2957750	0.85[EUR][1000 genomes]
rs3759820	0.86[EUR][1000 genomes]
rs3784309	0.88[YRI][hapmap]
rs3784310	0.89[CEU][hapmap];0.87[MEX][hapmap]
rs3784313	0.91[EUR][1000 genomes]
rs4511483	0.90[EUR][1000 genomes]
rs4526973	0.84[AFR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4777466	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62023343	0.93[EUR][1000 genomes]
rs6494973	1.00[CEU][hapmap];0.94[MEX][hapmap];0.95[TSI][hapmap];0.93[EUR][1000 genomes]
rs6494975	0.94[CEU][hapmap];0.84[EUR][1000 genomes]
rs7173626	0.92[EUR][1000 genomes]
rs7175373	0.87[EUR][1000 genomes]
rs7177242	0.94[CEU][hapmap];0.84[GIH][hapmap];0.81[MEX][hapmap];0.84[TSI][hapmap];0.81[EUR][1000 genomes]
rs7183748	0.82[EUR][1000 genomes]
rs7403191	0.82[EUR][1000 genomes]
rs7496582	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs7497104	1.00[CEU][hapmap];0.80[CHB][hapmap];0.89[GIH][hapmap];0.92[TSI][hapmap];0.93[EUR][1000 genomes]
rs8028115	0.84[EUR][1000 genomes]
rs8036307	0.93[EUR][1000 genomes]
rs8040216	1.00[CEU][hapmap];0.83[JPT][hapmap];0.85[EUR][1000 genomes]
rs8178	0.89[CEU][hapmap];0.84[EUR][1000 genomes]
rs8557	0.94[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9302260	0.93[EUR][1000 genomes]
rs982752	0.94[CEU][hapmap];0.82[GIH][hapmap];0.94[MEX][hapmap];0.87[TSI][hapmap];0.87[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	nsv904334	chr15:71737376-72177659	Strong transcription Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv1036938	chr15:71948106-72272855	Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Enhancers Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
3	esv3331306	chr15:72049818-72427559	Strong transcription ZNF genes & repeats Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
4	esv3433206	chr15:72049838-72427529	Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
5	nsv827383	chr15:72100044-72107239	Bivalent Enhancer Flanking Active TSS Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2415120	MYO9A	Cis_1M	lymphoblastoid	RTeQTL
rs2415120	TIPIN	cis	parietal	SCAN
rs2415120	PARP6	cis	parietal	SCAN
rs2415120	SENP8	cis	cerebellum	SCAN

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:72096000-72105600	Enhancers	Fetal Muscle Leg	muscle
2	chr15:72100400-72112000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr15:72100600-72111000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
4	chr15:72100600-72113800	Weak transcription	Fetal Lung	lung
5	chr15:72100800-72111400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr15:72101200-72112600	Weak transcription	Right Atrium	heart
7	chr15:72103000-72107400	Weak transcription	Fetal Brain Female	brain
8	chr15:72103400-72114000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr15:72104000-72105800	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr15:72104000-72106800	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr15:72104600-72105800	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr15:72104600-72107200	Strong transcription	Fetal Stomach	stomach
13	chr15:72104800-72105600	Enhancers	HSMMtube	muscle
14	chr15:72104800-72105800	Enhancers	Lung	lung
15	chr15:72104800-72109800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr15:72105000-72105600	Genic enhancers	Fetal Muscle Trunk	muscle
17	chr15:72105000-72106000	Enhancers	Right Ventricle	heart
18	chr15:72105000-72106000	Enhancers	Skeletal Muscle Male	skeletal muscle
19	chr15:72105200-72106000	Enhancers	Fetal Heart	heart
20	chr15:72105200-72106000	Enhancers	Skeletal Muscle Female	skeletal muscle
21	chr15:72105400-72105600	Enhancers	Placenta	Placenta

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