Variant report

Variant	rs2501930
Chromosome Location	chr9:78992324-78992325
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:78992210..78995895-chr9:78999208..79002045,3	MCF-7	breast:
2	chr9:78991796..78994850-chr9:78999374..79004024,5	K562	blood:
3	chr9:78991603..78996204-chr9:79007851..79009683,4	MCF-7	breast:
4	chr9:78991587..78996354-chr9:79007183..79010897,7	MCF-7	breast:
5	chr9:78991854..78994427-chr9:79006975..79009435,2	K562	blood:
6	chr8:117766615..117769384-chr9:78991570..78993615,2	MCF-7	breast:
7	chr9:78990957..78992471-chr9:78992875..78994908,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000135002	Chromatin interaction
ENSG00000147677	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10121699	0.90[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];0.84[MEX][hapmap];0.80[TSI][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10124695	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10735646	0.82[CHB][hapmap]
rs10869767	0.81[ASN][1000 genomes]
rs11144864	0.86[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs11144865	0.86[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs11144871	0.82[ASN][1000 genomes]
rs11788095	0.80[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs12057052	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13288968	0.97[ASN][1000 genomes]
rs13302654	0.86[ASN][1000 genomes]
rs1535845	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1961995	1.00[ASW][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];0.87[MKK][hapmap];0.85[TSI][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2002423	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2251604	0.82[ASN][1000 genomes]
rs2377639	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs2490572	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2490573	0.86[ASN][1000 genomes]
rs2490574	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2490576	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2490579	0.82[ASN][1000 genomes]
rs2490583	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2490584	0.84[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2490586	0.90[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2501920	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2501922	0.80[ASN][1000 genomes]
rs2501923	0.82[ASN][1000 genomes]
rs2501925	0.86[CHD][hapmap];0.95[JPT][hapmap];0.80[ASN][1000 genomes]
rs2501927	0.82[ASN][1000 genomes]
rs2501928	0.85[ASN][1000 genomes]
rs2501932	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2501933	0.86[ASN][1000 genomes]
rs2501935	0.86[ASN][1000 genomes]
rs2501937	0.94[ASN][1000 genomes]
rs2501938	0.94[ASN][1000 genomes]
rs2501939	0.96[ASN][1000 genomes]
rs2501940	0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2501942	0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3739729	0.82[ASN][1000 genomes]
rs4372070	1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs4745541	0.82[ASN][1000 genomes]
rs4745544	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4745545	0.85[ASN][1000 genomes]
rs4745546	0.86[ASN][1000 genomes]
rs6560522	0.95[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap]
rs7847608	0.90[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.80[TSI][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[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	chr9:78987600-79007800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr9:78988200-78993200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr9:78988200-79002600	Weak transcription	Skeletal Muscle Male	skeletal muscle
6	chr9:78988200-79003200	Weak transcription	HSMMtube	muscle
7	chr9:78988200-79008400	Weak transcription	Brain Substantia Nigra	brain
8	chr9:78988200-79008400	Weak transcription	Fetal Heart	heart
9	chr9:78988400-78999000	Weak transcription	Fetal Muscle Trunk	muscle
10	chr9:78988400-78999000	Weak transcription	Spleen	Spleen
11	chr9:78988400-78999600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
12	chr9:78988400-79002200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr9:78988600-78994200	Weak transcription	HMEC	breast
14	chr9:78988600-79001000	Weak transcription	HUES48 Cell Line	embryonic stem cell
15	chr9:78988600-79001000	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr9:78988600-79002400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr9:78988600-79007800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr9:78988600-79008200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr9:78988800-78999800	Weak transcription	Brain Anterior Caudate	brain
20	chr9:78988800-79006000	Weak transcription	Brain Angular Gyrus	brain
21	chr9:78988800-79007200	Weak transcription	Brain Hippocampus Middle	brain
22	chr9:78988800-79008400	Weak transcription	Brain Cingulate Gyrus	brain
23	chr9:78989000-78998200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr9:78989000-78999800	Weak transcription	GM12878-XiMat	blood
25	chr9:78989000-79000000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr9:78989000-79000200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr9:78989200-78997800	Weak transcription	Ovary	ovary
28	chr9:78989800-78995000	Weak transcription	Gastric	stomach
29	chr9:78989800-78999800	Weak transcription	Aorta	Aorta
30	chr9:78990000-78998600	Weak transcription	Colonic Mucosa	Colon
31	chr9:78990000-79005400	Weak transcription	Small Intestine	intestine
32	chr9:78990200-78999000	Weak transcription	Duodenum Smooth Muscle	Duodenum
33	chr9:78990200-79007800	Weak transcription	Fetal Brain Male	brain
34	chr9:78990200-79008400	Weak transcription	Right Ventricle	heart
35	chr9:78990400-78993800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr9:78990400-78994400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr9:78990400-78994600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
38	chr9:78990400-78994600	Weak transcription	Pancreas	Pancrea
39	chr9:78990400-78998400	Weak transcription	Adipose Nuclei	Adipose
40	chr9:78990400-78998800	Weak transcription	Primary hematopoietic stem cells	blood
41	chr9:78990400-78999000	Weak transcription	Sigmoid Colon	Sigmoid Colon
42	chr9:78990400-78999200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr9:78990400-78999200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr9:78990400-78999200	Weak transcription	Stomach Smooth Muscle	stomach
45	chr9:78990400-78999600	Weak transcription	Left Ventricle	heart
46	chr9:78990400-78999600	Weak transcription	HSMM	muscle
47	chr9:78990400-78999800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr9:78990400-78999800	Weak transcription	Fetal Muscle Leg	muscle
49	chr9:78990400-79001000	Weak transcription	HUES6 Cell Line	embryonic stem cell
50	chr9:78990400-79002600	Weak transcription	Esophagus	oesophagus

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