Variant report

Variant	rs2890985
Chromosome Location	chr9:14201586-14201587
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	chr9:14200461..14204358-chr9:14312033..14315867,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000147862	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10738355	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs10738356	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10756536	0.81[CHB][hapmap]
rs10756539	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10810106	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs10810110	0.86[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10810113	0.86[AMR][1000 genomes]
rs10810114	0.86[AMR][1000 genomes]
rs10961413	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs10961414	0.92[CEU][hapmap];0.81[EUR][1000 genomes]
rs10961420	0.83[ASN][1000 genomes]
rs12235129	0.91[EUR][1000 genomes]
rs13287487	0.91[CEU][hapmap]
rs2382448	0.84[CEU][hapmap];0.81[EUR][1000 genomes]
rs2382450	1.00[CEU][hapmap]
rs2382451	0.92[CEU][hapmap]
rs2382454	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs2382456	0.91[CEU][hapmap];0.93[EUR][1000 genomes]
rs2382457	1.00[CEU][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs2382458	0.92[CEU][hapmap];0.91[CHB][hapmap];0.83[JPT][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2382459	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2890982	0.81[CEU][hapmap]
rs2890984	1.00[CEU][hapmap];0.93[YRI][hapmap];0.83[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs4532695	0.83[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs4551459	0.92[CEU][hapmap]
rs4628344	0.92[CEU][hapmap];0.84[EUR][1000 genomes]
rs61754862	0.86[AMR][1000 genomes]
rs6474822	0.81[CHB][hapmap]
rs6474823	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs6474824	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs6474825	1.00[CEU][hapmap];0.91[YRI][hapmap];0.89[EUR][1000 genomes]
rs7034162	0.92[CEU][hapmap];0.84[EUR][1000 genomes]
rs7035474	0.81[CHB][hapmap]
rs73413827	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9776572	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1033764	chr9:13764918-14226168	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
2	nsv892593	chr9:13948798-14233159	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
3	nsv1023303	chr9:14025605-14286269	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
4	nsv540069	chr9:14025605-14286269	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
5	nsv1029491	chr9:14033607-14942373	Enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
6	nsv429998	chr9:14043516-14214688	Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
7	nsv892596	chr9:14145487-14208724	Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
8	nsv892597	chr9:14163383-14233159	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
9	nsv915804	chr9:14182608-14903050	Enhancers Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:14177200-14203400	Weak transcription	Fetal Muscle Trunk	muscle
2	chr9:14191800-14202800	Enhancers	Fetal Heart	heart
3	chr9:14192800-14207400	Weak transcription	Spleen	Spleen
4	chr9:14192800-14213400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr9:14193800-14203000	Enhancers	Fetal Brain Female	brain
6	chr9:14196000-14205400	Enhancers	Fetal Lung	lung
7	chr9:14197600-14202800	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr9:14197800-14201600	Enhancers	Right Ventricle	heart
9	chr9:14198200-14204000	Enhancers	Colon Smooth Muscle	Colon
10	chr9:14198600-14201600	Enhancers	Left Ventricle	heart
11	chr9:14198600-14201600	Enhancers	Psoas Muscle	Psoas
12	chr9:14198600-14203200	Enhancers	Breast Myoepithelial Primary Cells	Breast
13	chr9:14198800-14201600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr9:14199000-14209200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr9:14199200-14202200	Weak transcription	HSMMtube	muscle
16	chr9:14199200-14203200	Weak transcription	NHLF	lung
17	chr9:14199200-14209600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr9:14199400-14201600	Enhancers	Right Atrium	heart
19	chr9:14199400-14201600	Enhancers	HUVEC	blood vessel
20	chr9:14199400-14202800	Weak transcription	Brain Cingulate Gyrus	brain
21	chr9:14199400-14203000	Weak transcription	Duodenum Mucosa	Duodenum
22	chr9:14199400-14203200	Weak transcription	HSMM	muscle
23	chr9:14199400-14205600	Weak transcription	Small Intestine	intestine
24	chr9:14199400-14207400	Weak transcription	Esophagus	oesophagus
25	chr9:14199400-14207400	Weak transcription	Gastric	stomach
26	chr9:14199400-14209400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr9:14199400-14215800	Weak transcription	H1 Cell Line	embryonic stem cell
28	chr9:14199600-14202200	Weak transcription	NH-A	brain
29	chr9:14199600-14202400	Weak transcription	Brain Hippocampus Middle	brain
30	chr9:14199600-14202400	Enhancers	Stomach Smooth Muscle	stomach
31	chr9:14199600-14203000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
32	chr9:14199600-14203000	Weak transcription	Ovary	ovary
33	chr9:14199800-14202200	Weak transcription	Brain Germinal Matrix	brain
34	chr9:14199800-14202800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr9:14199800-14203000	Weak transcription	Brain Anterior Caudate	brain
36	chr9:14200000-14202200	Weak transcription	Brain Inferior Temporal Lobe	brain
37	chr9:14200000-14202800	Weak transcription	Brain Substantia Nigra	brain
38	chr9:14200000-14203000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr9:14200000-14203000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr9:14200000-14203000	Weak transcription	Muscle Satellite Cultured Cells	--
41	chr9:14200000-14203600	Weak transcription	A549	lung
42	chr9:14200200-14202400	Weak transcription	Liver	Liver
43	chr9:14200200-14202400	Weak transcription	Fetal Stomach	stomach
44	chr9:14200200-14202400	Weak transcription	Rectal Smooth Muscle	rectum
45	chr9:14200200-14202800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr9:14200200-14202800	Weak transcription	Osteobl	bone
47	chr9:14200200-14203000	Weak transcription	Stomach Mucosa	stomach
48	chr9:14200200-14203200	Weak transcription	Brain Angular Gyrus	brain
49	chr9:14200200-14203600	Weak transcription	Pancreas	Pancrea
50	chr9:14200200-14205400	Weak transcription	NHDF-Ad	bronchial

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