Variant report

Variant	rs12345849
Chromosome Location	chr9:6006293-6006294
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	MYC	chr9:6006013-6006445	MCF10A-Er-Src	breast:	n/a	n/a
2	MXI1	chr9:6005845-6009194	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:5827878..5830835-chr9:6005826..6008939,3	MCF-7	breast:
2	chr9:5957297..5958890-chr9:6003924..6006485,2	K562	blood:

Variant related genes	Relation type
MIR4665	TF binding region
ENSG00000099219	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10116214	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10125832	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10975350	0.81[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10975351	1.00[EUR][1000 genomes]
rs10975362	1.00[EUR][1000 genomes]
rs10975363	1.00[EUR][1000 genomes]
rs10975364	1.00[EUR][1000 genomes]
rs10975372	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10975377	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11506678	1.00[EUR][1000 genomes]
rs11793956	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs12337300	0.82[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs12337445	0.82[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs12337790	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12339713	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12339886	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12339889	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12340153	1.00[EUR][1000 genomes]
rs12340531	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12341021	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12342166	1.00[EUR][1000 genomes]
rs12342282	1.00[EUR][1000 genomes]
rs12343325	0.81[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs12351533	1.00[EUR][1000 genomes]
rs12352918	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1411949	1.00[EUR][1000 genomes]
rs1993912	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs28431078	1.00[EUR][1000 genomes]
rs28706504	1.00[EUR][1000 genomes]
rs386775	1.00[EUR][1000 genomes]
rs57154492	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58291302	1.00[EUR][1000 genomes]
rs60037728	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7022080	1.00[EUR][1000 genomes]
rs7029847	0.84[AFR][1000 genomes];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73383109	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73383113	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73383114	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73383144	0.84[AFR][1000 genomes];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73385128	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73387085	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73389036	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73389044	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73397307	1.00[EUR][1000 genomes]
rs73397376	1.00[EUR][1000 genomes]
rs73399307	1.00[EUR][1000 genomes]
rs73639554	1.00[EUR][1000 genomes]
rs73639568	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7853706	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7854980	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7858084	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7858846	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7875607	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9299025	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][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	nsv948847	chr9:5712626-6417677	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	nsv1031086	chr9:5806949-6630686	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats 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	42 gene(s)	inside rSNPs	diseases
3	nsv539967	chr9:5806949-6630686	Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
4	nsv892155	chr9:5825768-6044937	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
5	nsv892156	chr9:5892375-6011757	Weak transcription Genic enhancers Strong transcription Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
6	nsv1015450	chr9:5915640-6114652	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:5940000-6006800	Weak transcription	Gastric	stomach
2	chr9:5974000-6006800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr9:5977400-6006800	Weak transcription	Pancreas	Pancrea
4	chr9:5977400-6007000	Weak transcription	Spleen	Spleen
5	chr9:5989000-6006600	Weak transcription	Placenta	Placenta
6	chr9:5991800-6006800	Weak transcription	Esophagus	oesophagus
7	chr9:5999600-6007000	Weak transcription	Lung	lung
8	chr9:6003000-6006600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
9	chr9:6004000-6006600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
10	chr9:6004000-6006800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
11	chr9:6004200-6006600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
12	chr9:6005000-6006800	Weak transcription	Aorta	Aorta
13	chr9:6005400-6006400	Enhancers	Breast Myoepithelial Primary Cells	Breast
14	chr9:6005400-6006600	Enhancers	Primary T helper cells fromperipheralblood	blood
15	chr9:6005400-6006600	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr9:6005400-6006600	Flanking Active TSS	Brain Germinal Matrix	brain
17	chr9:6005600-6006400	Enhancers	Primary T cells from cord blood	blood
18	chr9:6005600-6006400	Enhancers	Primary hematopoietic stem cells	blood
19	chr9:6005600-6006400	Enhancers	Adipose Nuclei	Adipose
20	chr9:6005600-6006400	Flanking Active TSS	Fetal Brain Female	brain
21	chr9:6005600-6006400	Flanking Active TSS	Fetal Heart	heart
22	chr9:6005600-6006400	Weak transcription	Fetal Muscle Leg	muscle
23	chr9:6005600-6006400	Enhancers	Rectal Smooth Muscle	rectum
24	chr9:6005600-6006400	Flanking Active TSS	GM12878-XiMat	blood
25	chr9:6005600-6006400	Flanking Active TSS	NHLF	lung
26	chr9:6005600-6006600	Enhancers	Primary neutrophils fromperipheralblood	blood
27	chr9:6005600-6006600	Weak transcription	Primary T cells fromperipheralblood	blood
28	chr9:6005600-6006600	Enhancers	Colon Smooth Muscle	Colon
29	chr9:6005600-6006600	Flanking Active TSS	Pancreatic Islets	Pancreatic Islet
30	chr9:6005600-6006600	Flanking Active TSS	Hela-S3	cervix
31	chr9:6005600-6006800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr9:6005600-6006800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr9:6005600-6006800	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
34	chr9:6005600-6006800	Weak transcription	Fetal Muscle Trunk	muscle
35	chr9:6005600-6006800	Weak transcription	Left Ventricle	heart
36	chr9:6005600-6007000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr9:6005600-6007000	Weak transcription	Sigmoid Colon	Sigmoid Colon
38	chr9:6005600-6007200	Weak transcription	Small Intestine	intestine
39	chr9:6005600-6007400	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr9:6005600-6009200	Active TSS	HUES6 Cell Line	embryonic stem cell
41	chr9:6005800-6006400	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr9:6005800-6006400	Enhancers	Fetal Intestine Large	intestine
43	chr9:6005800-6006400	Enhancers	Fetal Stomach	stomach
44	chr9:6005800-6006400	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
45	chr9:6005800-6006400	Flanking Active TSS	Stomach Smooth Muscle	stomach
46	chr9:6005800-6006600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr9:6005800-6006600	Flanking Active TSS	Brain Hippocampus Middle	brain
48	chr9:6005800-6006600	Enhancers	Fetal Intestine Small	intestine
49	chr9:6005800-6006800	Enhancers	Primary monocytes fromperipheralblood	blood
50	chr9:6005800-6006800	Enhancers	Primary B cells from peripheral blood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links