Variant report

Variant	rs9409662
Chromosome Location	chr9:95002602-95002603
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:94902081..94903662-chr9:95000858..95003261,2	MCF-7	breast:
2	chr9:94895102..94897917-chr9:95001636..95003511,2	K562	blood:
3	chr9:94998465..95001053-chr9:95001549..95004769,3	K562	blood:
4	chr9:95000607..95005891-chr9:95055882..95059515,6	K562	blood:
5	chr9:94938776..94941220-chr9:95002439..95005177,2	K562	blood:

Variant related genes	Relation type
ENSG00000225511	Chromatin interaction
ENSG00000196305	Chromatin interaction

Extended variants
information (count: 71 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs10125510	0.89[EUR][1000 genomes]
rs1058726	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1058751	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10733744	0.89[EUR][1000 genomes]
rs10761159	0.89[EUR][1000 genomes]
rs1144933	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1152760	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1152761	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1152762	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1175737	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1175923	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1175929	0.98[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1175930	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1175931	0.84[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs11787696	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11788610	0.83[AFR][1000 genomes]
rs11789578	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11790257	0.82[ASN][1000 genomes]
rs11791931	0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs11792542	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11793505	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11794966	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12555097	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2084289	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2295939	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2398749	0.83[EUR][1000 genomes]
rs2761680	0.89[EUR][1000 genomes]
rs3894058	0.82[ASN][1000 genomes]
rs41280213	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs41280215	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs472163	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4743862	0.85[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs4743864	0.82[ASN][1000 genomes]
rs4743866	1.00[AFR][1000 genomes]
rs4743867	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4743868	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4743871	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4744123	0.82[ASN][1000 genomes]
rs4744124	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4744125	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs501814	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs556155	1.00[AFR][1000 genomes]
rs557066	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55894730	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs56110031	0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs56308715	0.85[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs56374228	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6479421	0.89[EUR][1000 genomes]
rs7042199	0.89[EUR][1000 genomes]
rs72748400	0.92[AFR][1000 genomes]
rs72748402	0.92[AFR][1000 genomes]
rs7864453	0.89[EUR][1000 genomes]
rs895639	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9409464	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9409465	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9409466	1.00[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs9409467	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9409469	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9409659	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9409660	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9409661	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9409663	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9409665	0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9409666	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs944949	0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949008	chr9:94500776-95182133	Enhancers ZNF genes & repeats Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
2	nsv1050845	chr9:94687959-95312406	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
3	nsv1046733	chr9:94690622-95138564	Genic enhancers Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
4	nsv530947	chr9:94697309-95093377	Weak transcription Bivalent Enhancer Strong transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
5	nsv917089	chr9:94857047-95099848	Weak transcription Flanking Bivalent TSS/Enh Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
6	nsv893573	chr9:94974188-95355719	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	33 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	chr9:94982800-95038400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr9:94982800-95045600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr9:94984000-95012400	Weak transcription	Stomach Mucosa	stomach
4	chr9:94990200-95003200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr9:94990200-95003200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr9:94990200-95004200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr9:94990200-95054000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr9:94990400-95004000	Strong transcription	Osteobl	bone
9	chr9:94990400-95004200	Strong transcription	NH-A	brain
10	chr9:94990400-95038200	Strong transcription	Primary T helper cells PMA-I stimulated	--
11	chr9:94990600-95004000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr9:94991000-95007000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr9:94991200-95006600	Strong transcription	HMEC	breast
14	chr9:94991200-95038400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr9:94991200-95052400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
16	chr9:94991200-95053600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
17	chr9:94991400-95004000	Weak transcription	Pancreatic Islets	Pancreatic Islet
18	chr9:94991400-95050400	Strong transcription	Dnd41	blood
19	chr9:94991400-95052400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr9:94991400-95053600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
21	chr9:94991400-95053800	Strong transcription	HUES48 Cell Line	embryonic stem cell
22	chr9:94991400-95053800	Strong transcription	HUES6 Cell Line	embryonic stem cell
23	chr9:94991600-95004000	Weak transcription	Fetal Brain Male	brain
24	chr9:94991800-95053800	Strong transcription	HUES64 Cell Line	embryonic stem cell
25	chr9:94991800-95054000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr9:94992200-95007800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr9:94994000-95004200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr9:94994000-95053000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr9:94994200-95038000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
30	chr9:94994400-95038600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
31	chr9:94994600-95003800	Strong transcription	Muscle Satellite Cultured Cells	--
32	chr9:94994600-95010800	Strong transcription	K562	blood
33	chr9:94994600-95051200	Strong transcription	Primary B cells from peripheral blood	blood
34	chr9:94995600-95038000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
35	chr9:94995600-95038600	Strong transcription	Primary T cells from cord blood	blood
36	chr9:94996000-95003200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr9:94996000-95004200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
38	chr9:94996000-95009800	Strong transcription	Fetal Intestine Small	intestine
39	chr9:94996000-95048600	Strong transcription	Fetal Stomach	stomach
40	chr9:94996200-95051400	Strong transcription	H1 Cell Line	embryonic stem cell
41	chr9:94996200-95051400	Strong transcription	Fetal Thymus	thymus
42	chr9:94996200-95052000	Strong transcription	Fetal Muscle Trunk	muscle
43	chr9:94996400-95051400	Strong transcription	Fetal Muscle Leg	muscle
44	chr9:94996400-95052000	Strong transcription	Duodenum Mucosa	Duodenum
45	chr9:94996600-95004200	Strong transcription	Liver	Liver
46	chr9:94996600-95006800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr9:94996600-95009800	Strong transcription	A549	lung
48	chr9:94996600-95011200	Strong transcription	GM12878-XiMat	blood
49	chr9:94996600-95035000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr9:94996600-95038400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood

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