Variant report

Variant	rs10521475
Chromosome Location	chr9:79267872-79267873
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SPI1	chr9:79267826-79268149	GM12891	blood:	n/a	chr9:79268035-79268044 chr9:79268033-79268046 chr9:79268032-79268045
2	GATA3	chr9:79267749-79268290	SK-N-SH	brain:	n/a	n/a
3	ELF1	chr9:79267868-79268119	K562	blood:	n/a	chr9:79268033-79268044
4	SPI1	chr9:79267838-79268190	HL-60	blood:	n/a	chr9:79268035-79268044 chr9:79268033-79268046 chr9:79268032-79268045
5	SPI1	chr9:79267832-79268155	GM12891	blood:	n/a	chr9:79268035-79268044 chr9:79268033-79268046 chr9:79268032-79268045
6	GATA3	chr9:79267617-79268312	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:79073774..79075631-chr9:79267070..79269675,2	MCF-7	breast:

Variant related genes	Relation type
PRUNE2	TF binding region
ENSG00000187210	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs11144986	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[CHD][hapmap];0.84[MKK][hapmap];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11144987	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11144992	1.00[CEU][hapmap];0.92[CHB][hapmap];0.90[JPT][hapmap];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11144996	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17062768	1.00[CEU][hapmap]
rs17062772	1.00[CEU][hapmap]
rs17062775	1.00[CEU][hapmap]
rs17062778	1.00[CEU][hapmap]
rs17062858	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.92[GIH][hapmap];0.91[JPT][hapmap];0.80[MKK][hapmap];0.81[YRI][hapmap];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1854441	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[CHD][hapmap];0.92[GIH][hapmap];0.91[JPT][hapmap];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1952460	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.88[YRI][hapmap];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2067501	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.95[ASN][1000 genomes]
rs499746	1.00[CEU][hapmap]
rs57389265	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs634063	0.93[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs637207	1.00[CEU][hapmap]
rs644893	1.00[CEU][hapmap]
rs7027074	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7028756	0.91[ASN][1000 genomes]
rs7038619	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7039310	1.00[CHB][hapmap];0.90[JPT][hapmap];0.92[ASN][1000 genomes]
rs7045505	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];0.83[GIH][hapmap];0.90[JPT][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7847922	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7859873	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][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	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	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
4	nsv949417	chr9:79078703-79282589	Strong transcription Genic enhancers Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
5	nsv1040363	chr9:79246366-79711737	Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:81 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:79252600-79278000	Weak transcription	Gastric	stomach
2	chr9:79258000-79270000	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr9:79259000-79269200	Weak transcription	Brain Substantia Nigra	brain
4	chr9:79259000-79278000	Weak transcription	Spleen	Spleen
5	chr9:79260000-79282400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr9:79263600-79268600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
7	chr9:79263600-79268600	Weak transcription	Aorta	Aorta
8	chr9:79263600-79272800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr9:79263600-79282200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr9:79265400-79268200	Enhancers	HUES6 Cell Line	embryonic stem cell
11	chr9:79265400-79268600	Enhancers	Muscle Satellite Cultured Cells	--
12	chr9:79265400-79269200	Genic enhancers	HSMM	muscle
13	chr9:79265400-79270800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr9:79265600-79268000	Enhancers	Colon Smooth Muscle	Colon
15	chr9:79265600-79268200	Enhancers	GM12878-XiMat	blood
16	chr9:79265600-79268400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
17	chr9:79265600-79269600	Weak transcription	Brain Angular Gyrus	brain
18	chr9:79265600-79270600	Enhancers	Fetal Thymus	thymus
19	chr9:79265600-79270600	Enhancers	NHLF	lung
20	chr9:79265600-79274000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr9:79265800-79268800	Weak transcription	Fetal Heart	heart
22	chr9:79266000-79268200	Weak transcription	NH-A	brain
23	chr9:79266000-79268400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr9:79266000-79268800	Weak transcription	Stomach Mucosa	stomach
25	chr9:79266000-79278000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr9:79266200-79268600	Weak transcription	Fetal Kidney	kidney
27	chr9:79266400-79268400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr9:79266400-79268400	Weak transcription	NHDF-Ad	bronchial
29	chr9:79266400-79268800	Weak transcription	Fetal Muscle Leg	muscle
30	chr9:79266400-79269200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
31	chr9:79266400-79269800	Weak transcription	Brain Hippocampus Middle	brain
32	chr9:79266400-79269800	Enhancers	Osteobl	bone
33	chr9:79266400-79271400	Enhancers	Primary neutrophils fromperipheralblood	blood
34	chr9:79266400-79272000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
35	chr9:79266400-79306800	Weak transcription	Fetal Stomach	stomach
36	chr9:79266600-79268200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr9:79266600-79269800	Weak transcription	Pancreatic Islets	Pancreatic Islet
38	chr9:79266600-79270400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
39	chr9:79266600-79274200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr9:79266600-79282200	Weak transcription	Brain Anterior Caudate	brain
41	chr9:79266800-79268000	Enhancers	Primary B cells from peripheral blood	blood
42	chr9:79266800-79268600	Weak transcription	Ovary	ovary
43	chr9:79266800-79269000	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr9:79266800-79269400	Enhancers	Primary monocytes fromperipheralblood	blood
45	chr9:79266800-79269600	Enhancers	Primary B cells from cord blood	blood
46	chr9:79266800-79269800	Enhancers	HUVEC	blood vessel
47	chr9:79266800-79272600	Enhancers	Primary hematopoietic stem cells	blood
48	chr9:79267000-79269000	Strong transcription	Brain Inferior Temporal Lobe	brain
49	chr9:79267000-79269200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
50	chr9:79267000-79269600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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