Variant report

Variant	rs7852884
Chromosome Location	chr9:78990982-78990983
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:78990957..78992471-chr9:78992875..78994908,2	MCF-7	breast:

Extended variants
information (count: 72 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs10116800	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10118954	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10119732	0.95[ASN][1000 genomes]
rs10125012	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10125667	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10781358	1.00[ASN][1000 genomes]
rs10781359	0.95[ASN][1000 genomes]
rs10781360	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10869770	1.00[ASN][1000 genomes]
rs10869774	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11144870	1.00[ASN][1000 genomes]
rs11144875	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11144878	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11144881	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11144887	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11144894	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11144897	0.95[ASN][1000 genomes]
rs1129399	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11548954	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11791951	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11793613	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11794019	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12156473	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12375735	0.86[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs12377856	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12377878	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12380332	0.84[ASN][1000 genomes]
rs12380522	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1324213	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1951910	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2377640	0.86[AMR][1000 genomes]
rs2377641	0.84[AMR][1000 genomes]
rs3187236	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4571791	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs55740812	0.94[ASN][1000 genomes]
rs57339182	0.84[ASN][1000 genomes]
rs57480680	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58136435	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs59424752	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61334567	0.86[AMR][1000 genomes]
rs62564441	0.90[ASN][1000 genomes]
rs62564442	0.90[ASN][1000 genomes]
rs62564446	0.84[ASN][1000 genomes]
rs62565109	0.83[ASN][1000 genomes]
rs62567918	0.94[ASN][1000 genomes]
rs62567919	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62568690	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62568692	1.00[ASN][1000 genomes]
rs6560513	0.86[AMR][1000 genomes]
rs6560515	0.86[AMR][1000 genomes]
rs6560516	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7023191	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7025942	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7026067	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7029439	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7035385	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7037345	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7038009	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7038056	0.90[ASN][1000 genomes]
rs7040138	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7041690	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7047489	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7049245	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7851616	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7853410	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7854540	0.84[ASN][1000 genomes]
rs7859327	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7875575	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869152	chr9:78742197-79583399	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv931033	chr9:78850330-79366454	Genic enhancers Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv893478	chr9:78933874-79101006	Weak transcription Genic enhancers Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
4	nsv893479	chr9:78971253-79275226	Weak transcription Strong transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:78984600-78993200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr9:78986600-79008400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr9:78986800-78991000	Enhancers	Fetal Stomach	stomach
4	chr9:78987000-78991000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr9:78987200-78991200	Enhancers	Stomach Mucosa	stomach
6	chr9:78987600-79007800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr9:78988200-78993200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr9:78988200-79002600	Weak transcription	Skeletal Muscle Male	skeletal muscle
9	chr9:78988200-79003200	Weak transcription	HSMMtube	muscle
10	chr9:78988200-79008400	Weak transcription	Brain Substantia Nigra	brain
11	chr9:78988200-79008400	Weak transcription	Fetal Heart	heart
12	chr9:78988400-78999000	Weak transcription	Fetal Muscle Trunk	muscle
13	chr9:78988400-78999000	Weak transcription	Spleen	Spleen
14	chr9:78988400-78999600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
15	chr9:78988400-79002200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr9:78988600-78994200	Weak transcription	HMEC	breast
17	chr9:78988600-79001000	Weak transcription	HUES48 Cell Line	embryonic stem cell
18	chr9:78988600-79001000	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr9:78988600-79002400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr9:78988600-79007800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
21	chr9:78988600-79008200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr9:78988800-78999800	Weak transcription	Brain Anterior Caudate	brain
23	chr9:78988800-79006000	Weak transcription	Brain Angular Gyrus	brain
24	chr9:78988800-79007200	Weak transcription	Brain Hippocampus Middle	brain
25	chr9:78988800-79008400	Weak transcription	Brain Cingulate Gyrus	brain
26	chr9:78989000-78998200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr9:78989000-78999800	Weak transcription	GM12878-XiMat	blood
28	chr9:78989000-79000000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr9:78989000-79000200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr9:78989200-78997800	Weak transcription	Ovary	ovary
31	chr9:78989600-78991800	Enhancers	HUVEC	blood vessel
32	chr9:78989800-78991600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr9:78989800-78995000	Weak transcription	Gastric	stomach
34	chr9:78989800-78999800	Weak transcription	Aorta	Aorta
35	chr9:78990000-78991800	Weak transcription	Pancreatic Islets	Pancreatic Islet
36	chr9:78990000-78998600	Weak transcription	Colonic Mucosa	Colon
37	chr9:78990000-79005400	Weak transcription	Small Intestine	intestine
38	chr9:78990200-78999000	Weak transcription	Duodenum Smooth Muscle	Duodenum
39	chr9:78990200-79007800	Weak transcription	Fetal Brain Male	brain
40	chr9:78990200-79008400	Weak transcription	Right Ventricle	heart
41	chr9:78990400-78993800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr9:78990400-78994400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr9:78990400-78994600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
44	chr9:78990400-78994600	Weak transcription	Pancreas	Pancrea
45	chr9:78990400-78998400	Weak transcription	Adipose Nuclei	Adipose
46	chr9:78990400-78998800	Weak transcription	Primary hematopoietic stem cells	blood
47	chr9:78990400-78999000	Weak transcription	Sigmoid Colon	Sigmoid Colon
48	chr9:78990400-78999200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr9:78990400-78999200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr9:78990400-78999200	Weak transcription	Stomach Smooth Muscle	stomach

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