Variant report

Variant	rs753023
Chromosome Location	chr9:72820398-72820399
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	chr9:72805117..72807381-chr9:72819423..72821508,2	MCF-7	breast:

Extended variants
information (count: 89 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:88)

rs_ID	r²[population]
rs10114215	0.86[ASN][1000 genomes]
rs10491653	0.87[AMR][1000 genomes]
rs1073540	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12683706	1.00[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12683986	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12684301	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12684987	1.00[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12685322	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12685441	1.00[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12685491	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12685534	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12686312	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12686573	1.00[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12686584	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12686850	1.00[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17051690	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17051696	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17052443	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17052748	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17053503	0.87[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs17088796	1.00[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs17088840	1.00[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs17088889	1.00[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17088905	1.00[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1927116	1.00[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1927117	1.00[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1927119	1.00[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1927142	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1927143	0.91[ASN][1000 genomes]
rs1927148	0.95[ASN][1000 genomes]
rs1927150	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2026138	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2094400	0.87[AMR][1000 genomes]
rs2148853	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2148865	1.00[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2182731	0.81[ASN][1000 genomes]
rs2182732	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2296772	1.00[AMR][1000 genomes]
rs2296773	1.00[AMR][1000 genomes]
rs2871290	0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2871295	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3015223	1.00[AMR][1000 genomes]
rs34061327	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35188046	1.00[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35508139	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3739773	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3739774	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4069793	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4287005	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4410968	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4439194	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4495496	1.00[AMR][1000 genomes]
rs4596711	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4602958	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4606121	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4610818	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4621877	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4744982	0.88[ASN][1000 genomes]
rs56735283	1.00[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56860643	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57048128	1.00[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs57398306	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57477024	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs58219953	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs58662316	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs58948879	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs58969772	0.93[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs58976318	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs59010963	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs59189596	0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs59444215	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs59546243	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs59589460	1.00[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs59619263	1.00[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs59960592	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs59976188	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs60049462	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs60391643	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs60458589	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61092050	0.87[AMR][1000 genomes]
rs61265226	1.00[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7022893	0.86[ASN][1000 genomes]
rs7046167	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs716535	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs753022	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7875348	0.88[ASN][1000 genomes]
rs943540	0.94[ASN][1000 genomes]
rs954808	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1047862	chr9:72746875-73138287	Enhancers Strong transcription Genic enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats 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	66 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs753023	MAMDC2,RPL24	cis	brain	BrainEAC

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:72793000-72842600	Weak transcription	Rectal Smooth Muscle	rectum
2	chr9:72802000-72827000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr9:72808000-72820400	Weak transcription	Left Ventricle	heart
4	chr9:72809400-72820400	Weak transcription	HSMM	muscle
5	chr9:72809600-72837800	Weak transcription	NH-A	brain
6	chr9:72810800-72827800	Weak transcription	Colon Smooth Muscle	Colon
7	chr9:72811400-72820400	Weak transcription	Duodenum Smooth Muscle	Duodenum
8	chr9:72812000-72820400	Weak transcription	Stomach Smooth Muscle	stomach
9	chr9:72813000-72820400	Weak transcription	HSMMtube	muscle
10	chr9:72819200-72820600	Enhancers	H1 Cell Line	embryonic stem cell
11	chr9:72819600-72820400	Active TSS	HUES6 Cell Line	embryonic stem cell
12	chr9:72819600-72820400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr9:72819600-72821000	Enhancers	iPS-18 Cell Line	embryonic stem cell
14	chr9:72819600-72821000	ZNF genes & repeats	Liver	Liver
15	chr9:72819800-72820600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr9:72820000-72820400	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
17	chr9:72820000-72820400	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr9:72820000-72820600	Enhancers	HUES48 Cell Line	embryonic stem cell
19	chr9:72820000-72820600	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr9:72820000-72820600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr9:72820000-72820800	Enhancers	Placenta Amnion	Placenta Amnion
22	chr9:72820000-72820800	Flanking Active TSS	NHEK	skin
23	chr9:72820000-72821200	Enhancers	Fetal Lung	lung
24	chr9:72820000-72821400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr9:72820000-72821600	Enhancers	Cortex derived primary cultured neurospheres	brain
26	chr9:72820200-72820400	Weak transcription	Skeletal Muscle Male	skeletal muscle
27	chr9:72820200-72820400	Flanking Active TSS	HMEC	breast
28	chr9:72820200-72820600	Enhancers	iPS-15b Cell Line	embryonic stem cell
29	chr9:72820200-72821200	Enhancers	Breast Myoepithelial Primary Cells	Breast
30	chr9:72820200-72821200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain

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