Variant report

Variant	rs7038564
Chromosome Location	chr9:96313012-96313013
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	chr9:96299951..96301653-chr9:96312978..96315917,2	MCF-7	breast:

Extended variants
information (count: 59 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10046907	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10119832	0.86[EUR][1000 genomes]
rs10122014	1.00[CHB][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.86[EUR][1000 genomes]
rs10124517	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10512224	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs10512226	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12552189	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12553275	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1317260	1.00[CHB][hapmap];0.82[JPT][hapmap];0.86[EUR][1000 genomes]
rs13286188	0.85[CHB][hapmap]
rs1331588	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs16909211	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2250236	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs2254715	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs2274851	0.86[EUR][1000 genomes]
rs28403269	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2994366	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2994368	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs3897285	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4146138	1.00[CHB][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes]
rs4573340	0.81[EUR][1000 genomes]
rs55649770	0.81[EUR][1000 genomes]
rs55702483	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs55812345	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs55934002	0.81[EUR][1000 genomes]
rs56375911	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs57303681	0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs57631285	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs58782393	0.81[EUR][1000 genomes]
rs58790127	0.81[EUR][1000 genomes]
rs60212988	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs60253984	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60610533	0.83[ASN][1000 genomes]
rs60650773	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61340241	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6479494	0.88[ASW][hapmap];0.98[LWK][hapmap];0.91[MKK][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes]
rs6479495	0.95[AFR][1000 genomes]
rs7020195	0.82[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs7025805	0.89[LWK][hapmap]
rs7033849	1.00[CHB][hapmap]
rs7044283	1.00[CHB][hapmap];0.86[EUR][1000 genomes]
rs73651206	0.81[EUR][1000 genomes]
rs73651227	0.81[EUR][1000 genomes]
rs73651228	0.81[EUR][1000 genomes]
rs73651229	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73651232	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73651246	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73651248	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73651271	0.86[EUR][1000 genomes]
rs7854217	0.81[EUR][1000 genomes]
rs7854349	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7857165	1.00[CHB][hapmap];0.82[JPT][hapmap];0.82[EUR][1000 genomes]
rs7861929	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7874126	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs914417	1.00[CHB][hapmap]
rs9299409	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs999326	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1041803	chr9:96299639-96342013	Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	nsv824984	chr9:96310933-96375022	Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:96278400-96327000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
2	chr9:96278400-96327200	Strong transcription	Primary monocytes fromperipheralblood	blood
3	chr9:96278400-96328200	Strong transcription	Monocytes-CD14+_RO01746	blood
4	chr9:96279000-96327400	Strong transcription	Primary T helper cells fromperipheralblood	blood
5	chr9:96282200-96323400	Strong transcription	Primary B cells from cord blood	blood
6	chr9:96284600-96327200	Strong transcription	Primary T helper cells PMA-I stimulated	--
7	chr9:96284600-96328200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr9:96284800-96327200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr9:96285000-96327000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr9:96285000-96327000	Strong transcription	Dnd41	blood
11	chr9:96285200-96327800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr9:96285400-96327800	Strong transcription	Liver	Liver
13	chr9:96289200-96316000	Strong transcription	HUES64 Cell Line	embryonic stem cell
14	chr9:96291800-96317000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr9:96291800-96317000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr9:96292000-96316600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr9:96295800-96315600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
18	chr9:96299200-96326800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr9:96299400-96324200	Weak transcription	Fetal Brain Male	brain
20	chr9:96299400-96327800	Strong transcription	Placenta	Placenta
21	chr9:96300400-96322400	Strong transcription	Primary T cells fromperipheralblood	blood
22	chr9:96300600-96313200	Strong transcription	Primary T cells from cord blood	blood
23	chr9:96301200-96327200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
24	chr9:96302000-96328000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr9:96302600-96315800	Strong transcription	Fetal Lung	lung
26	chr9:96304400-96328200	Strong transcription	Adipose Nuclei	Adipose
27	chr9:96304600-96315600	Strong transcription	HUES48 Cell Line	embryonic stem cell
28	chr9:96305200-96326800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
29	chr9:96305200-96327000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
30	chr9:96305400-96327000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr9:96305400-96327200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr9:96305400-96327600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr9:96305600-96315400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
34	chr9:96305800-96314200	Weak transcription	Psoas Muscle	Psoas
35	chr9:96305800-96317000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
36	chr9:96305800-96319800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
37	chr9:96307600-96329000	Weak transcription	Right Atrium	heart
38	chr9:96308800-96324200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr9:96309000-96314800	Weak transcription	Brain Substantia Nigra	brain
40	chr9:96309000-96318200	Weak transcription	Rectal Smooth Muscle	rectum
41	chr9:96309200-96314200	Weak transcription	H1 Cell Line	embryonic stem cell
42	chr9:96309200-96314200	Weak transcription	Esophagus	oesophagus
43	chr9:96309200-96314200	Weak transcription	NH-A	brain
44	chr9:96309200-96316400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr9:96309200-96317000	Weak transcription	Colonic Mucosa	Colon
46	chr9:96309200-96319000	Weak transcription	Brain Angular Gyrus	brain
47	chr9:96309400-96317600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
48	chr9:96309600-96314200	Weak transcription	Brain Hippocampus Middle	brain
49	chr9:96309600-96320200	Weak transcription	Placenta Amnion	Placenta Amnion
50	chr9:96309800-96314200	Weak transcription	Thymus	Thymus

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