Variant report

Variant	rs12345094
Chromosome Location	chr9:26921623-26921624
allele	A/G
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	STAT3	chr9:26921489-26921662	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:26891289..26894164-chr9:26921199..26924471,3	MCF-7	breast:
2	chr9:26920077..26923896-chr9:26945076..26948067,5	MCF-7	breast:

Variant related genes	Relation type
PLAA	TF binding region
ENSG00000096872	Chromatin interaction
ENSG00000120159	Chromatin interaction
ENSG00000137055	Chromatin interaction

Extended variants
information (count: 86 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:85)

rs_ID	r²[population]
rs10217792	1.00[YRI][hapmap]
rs10283496	0.84[AFR][1000 genomes]
rs10283643	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1048949	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10511793	1.00[CHB][hapmap]
rs10812492	1.00[CHB][hapmap]
rs10812500	1.00[CHB][hapmap]
rs10967592	1.00[YRI][hapmap];0.84[AFR][1000 genomes]
rs10967593	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs10967594	1.00[CHB][hapmap]
rs10967595	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10967596	1.00[YRI][hapmap];0.84[AFR][1000 genomes]
rs10967606	0.84[AFR][1000 genomes]
rs10967607	0.84[AFR][1000 genomes]
rs10967624	1.00[CHB][hapmap];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10967625	1.00[CHB][hapmap]
rs10967634	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10967638	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10967639	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10967640	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10967644	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1161603	1.00[CHB][hapmap]
rs11999015	1.00[ASN][1000 genomes]
rs12001845	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12002068	1.00[ASN][1000 genomes]
rs12003612	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12336131	1.00[YRI][hapmap];0.84[AFR][1000 genomes]
rs12336425	0.84[AFR][1000 genomes]
rs12337864	0.84[AFR][1000 genomes]
rs12338421	1.00[YRI][hapmap];0.84[AFR][1000 genomes]
rs12338678	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12338827	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12339063	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12341319	0.84[AFR][1000 genomes]
rs12341560	1.00[YRI][hapmap];0.84[AFR][1000 genomes]
rs12341712	1.00[YRI][hapmap]
rs12342005	1.00[CHB][hapmap]
rs12343349	0.84[AFR][1000 genomes]
rs12343386	0.84[AFR][1000 genomes]
rs12346262	1.00[YRI][hapmap]
rs12346926	1.00[YRI][hapmap]
rs12348209	0.84[AFR][1000 genomes]
rs12348249	0.84[AFR][1000 genomes]
rs12349359	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12352441	1.00[CHB][hapmap]
rs16910755	1.00[AMR][1000 genomes]
rs16910832	0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs16910834	0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs16910888	1.00[CHB][hapmap]
rs16910895	1.00[CHB][hapmap]
rs17694121	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17694140	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17694300	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17694306	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17694549	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17755398	1.00[AMR][1000 genomes]
rs17755820	1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs17755887	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17755911	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17756221	1.00[JPT][hapmap];0.90[EUR][1000 genomes]
rs17760378	1.00[JPT][hapmap]
rs2152063	1.00[CHB][hapmap]
rs2991949	1.00[CHB][hapmap]
rs3429	1.00[CHB][hapmap]
rs41271173	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41272237	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs41272239	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs55902149	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs59478807	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs596427	1.00[CHB][hapmap]
rs59757728	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61331313	1.00[ASN][1000 genomes]
rs615532	1.00[CHB][hapmap]
rs6475948	1.00[CHB][hapmap]
rs7037860	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7039400	1.00[CHB][hapmap]
rs7040516	1.00[CHB][hapmap]
rs73433963	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73643117	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73643119	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73643120	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73643125	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7871097	1.00[CHB][hapmap]
rs7871286	1.00[CHB][hapmap]
rs892570	1.00[AMR][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	nsv528614	chr9:26893662-27074233	Flanking Active TSS Strong transcription Weak transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 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	chr9:26893000-26922600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr9:26893000-26924200	Weak transcription	Esophagus	oesophagus
3	chr9:26893200-26923200	Weak transcription	Right Ventricle	heart
4	chr9:26893400-26925000	Weak transcription	Stomach Mucosa	stomach
5	chr9:26893400-26936400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr9:26893400-26936400	Weak transcription	Psoas Muscle	Psoas
7	chr9:26898200-26924400	Weak transcription	Aorta	Aorta
8	chr9:26900800-26930000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr9:26901200-26935800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr9:26902800-26936600	Weak transcription	Spleen	Spleen
11	chr9:26903000-26927800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr9:26903000-26929800	Strong transcription	HUES64 Cell Line	embryonic stem cell
13	chr9:26903000-26935200	Strong transcription	Monocytes-CD14+_RO01746	blood
14	chr9:26903200-26928400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
15	chr9:26903200-26930000	Strong transcription	HUES48 Cell Line	embryonic stem cell
16	chr9:26903200-26932600	Strong transcription	Dnd41	blood
17	chr9:26903200-26935200	Strong transcription	Primary monocytes fromperipheralblood	blood
18	chr9:26903800-26927800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr9:26903800-26931600	Strong transcription	HUES6 Cell Line	embryonic stem cell
20	chr9:26904600-26935200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr9:26905400-26938200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr9:26905800-26937400	Weak transcription	Pancreatic Islets	Pancreatic Islet
23	chr9:26906200-26928800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr9:26906200-26936600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
25	chr9:26909200-26925200	Weak transcription	K562	blood
26	chr9:26911200-26926000	Strong transcription	Primary T cells from cord blood	blood
27	chr9:26911600-26930000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr9:26911600-26930000	Strong transcription	Placenta	Placenta
29	chr9:26912000-26928600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
30	chr9:26912000-26932600	Strong transcription	Primary T cells fromperipheralblood	blood
31	chr9:26912800-26928000	Strong transcription	Primary neutrophils fromperipheralblood	blood
32	chr9:26912800-26935000	Strong transcription	Primary T helper cells fromperipheralblood	blood
33	chr9:26913200-26928400	Strong transcription	NH-A	brain
34	chr9:26913200-26932600	Strong transcription	Primary B cells from cord blood	blood
35	chr9:26913400-26928000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
36	chr9:26913600-26927400	Strong transcription	Fetal Thymus	thymus
37	chr9:26913600-26928000	Strong transcription	Rectal Mucosa Donor 31	rectum
38	chr9:26913600-26928600	Strong transcription	GM12878-XiMat	blood
39	chr9:26914200-26928800	Strong transcription	Brain Inferior Temporal Lobe	brain
40	chr9:26914600-26930000	Strong transcription	Skeletal Muscle Female	skeletal muscle
41	chr9:26914600-26935600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr9:26914800-26921800	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr9:26915000-26926800	Strong transcription	Muscle Satellite Cultured Cells	--
44	chr9:26915000-26927000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
45	chr9:26915000-26928600	Strong transcription	Duodenum Smooth Muscle	Duodenum
46	chr9:26915200-26926000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
47	chr9:26915200-26928800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr9:26915200-26929000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr9:26915200-26929600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr9:26915200-26929600	Strong transcription	Liver	Liver

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