Variant report

Variant	rs12343325
Chromosome Location	chr9:5926592-5926593
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	chr9:5925409..5927394-chr9:5940520..5942739,2	MCF-7	breast:

Extended variants
information (count: 62 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10116214	1.00[EUR][1000 genomes]
rs10125832	0.81[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10975350	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10975351	0.82[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10975362	1.00[EUR][1000 genomes]
rs10975363	1.00[EUR][1000 genomes]
rs10975364	1.00[EUR][1000 genomes]
rs10975367	1.00[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs10975372	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10975377	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11506678	1.00[EUR][1000 genomes]
rs11793956	0.90[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs12337300	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12337445	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12337790	1.00[EUR][1000 genomes]
rs12339713	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12339886	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12339889	1.00[EUR][1000 genomes]
rs12340153	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12340531	1.00[EUR][1000 genomes]
rs12341021	1.00[EUR][1000 genomes]
rs12342166	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12342282	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12345849	0.81[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs12351533	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1411949	1.00[EUR][1000 genomes]
rs1993912	0.90[AFR][1000 genomes]
rs28431078	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28706504	1.00[EUR][1000 genomes]
rs57154492	1.00[EUR][1000 genomes]
rs58291302	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60037728	1.00[EUR][1000 genomes]
rs7022080	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7029847	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73383109	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73383113	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73383114	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73383144	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73385128	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73387085	0.88[AFR][1000 genomes]
rs73389036	1.00[EUR][1000 genomes]
rs73389044	1.00[EUR][1000 genomes]
rs73397307	0.84[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73397376	0.82[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73399307	0.82[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73639554	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73639568	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7853706	0.88[AFR][1000 genomes]
rs7854980	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7858084	0.81[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs7858846	0.81[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs7874032	1.00[ASN][1000 genomes]
rs7875607	1.00[EUR][1000 genomes]
rs9299025	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1017103	chr9:5509431-5987907	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Genic enhancers 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 target site	31 gene(s)	inside rSNPs	diseases
2	nsv539965	chr9:5509431-5987907	ZNF genes & repeats Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	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
4	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
5	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
6	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
7	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
8	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:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:5898400-5947200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
2	chr9:5918400-5928400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr9:5918800-5928800	Weak transcription	Stomach Mucosa	stomach
4	chr9:5919000-5939800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr9:5919800-5927600	Strong transcription	Adipose Nuclei	Adipose
6	chr9:5919800-5929400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr9:5919800-5935600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr9:5920000-5927200	Strong transcription	Primary monocytes fromperipheralblood	blood
9	chr9:5920000-5929200	Strong transcription	Monocytes-CD14+_RO01746	blood
10	chr9:5920800-5931200	Weak transcription	A549	lung
11	chr9:5920800-5938800	Weak transcription	Small Intestine	intestine
12	chr9:5921200-5927400	Strong transcription	Primary T helper cells fromperipheralblood	blood
13	chr9:5921200-5939800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr9:5921200-5950400	Weak transcription	Psoas Muscle	Psoas
15	chr9:5922000-5941600	Weak transcription	HSMMtube	muscle
16	chr9:5922200-5935800	Weak transcription	Colon Smooth Muscle	Colon
17	chr9:5922400-5933400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
18	chr9:5922400-5935000	Weak transcription	Pancreas	Pancrea
19	chr9:5922400-5935200	Weak transcription	HMEC	breast
20	chr9:5922400-5939800	Weak transcription	Gastric	stomach
21	chr9:5922600-5947000	Weak transcription	Fetal Heart	heart
22	chr9:5923000-5927200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
23	chr9:5923000-5928400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
24	chr9:5923000-5936200	Weak transcription	Muscle Satellite Cultured Cells	--
25	chr9:5923000-5945200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
26	chr9:5923000-5969000	Weak transcription	Fetal Stomach	stomach
27	chr9:5923200-5933400	Weak transcription	Left Ventricle	heart
28	chr9:5923200-5933600	Weak transcription	Fetal Lung	lung
29	chr9:5923200-5934000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
30	chr9:5923200-5934200	Weak transcription	Colonic Mucosa	Colon
31	chr9:5923200-5934800	Weak transcription	Dnd41	blood
32	chr9:5923200-5935000	Weak transcription	Spleen	Spleen
33	chr9:5923200-5935000	Weak transcription	HepG2	liver
34	chr9:5923200-5935200	Weak transcription	Skeletal Muscle Male	skeletal muscle
35	chr9:5923200-5935800	Weak transcription	HUVEC	blood vessel
36	chr9:5923200-5938800	Weak transcription	Right Ventricle	heart
37	chr9:5923200-5939000	Weak transcription	Lung	lung
38	chr9:5923200-5939600	Weak transcription	Brain Angular Gyrus	brain
39	chr9:5923200-5943000	Weak transcription	Esophagus	oesophagus
40	chr9:5923200-5947600	Weak transcription	Fetal Kidney	kidney
41	chr9:5923200-5949200	Weak transcription	NHLF	lung
42	chr9:5923200-5968200	Weak transcription	Fetal Muscle Leg	muscle
43	chr9:5923200-5971800	Weak transcription	NHEK	skin
44	chr9:5923200-5972400	Weak transcription	Aorta	Aorta
45	chr9:5923400-5927200	Weak transcription	Ovary	ovary
46	chr9:5923400-5927600	Weak transcription	GM12878-XiMat	blood
47	chr9:5923400-5931600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
48	chr9:5923400-5933400	Weak transcription	Thymus	Thymus
49	chr9:5923400-5935800	Weak transcription	HUES6 Cell Line	embryonic stem cell
50	chr9:5923400-5939400	Weak transcription	Brain Inferior Temporal Lobe	brain

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