Variant report

Variant	rs2890984
Chromosome Location	chr9:14198747-14198748
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:14197932..14199524-chr9:14315702..14317595,2	MCF-7	breast:
2	chr9:14198598..14200536-chr9:14204416..14206854,2	MCF-7	breast:
3	chr9:14185623..14188206-chr9:14197745..14200671,2	MCF-7	breast:
4	chr9:14198108..14200232-chr9:14207218..14209041,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000225472	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10738355	1.00[CEU][hapmap];0.90[CHB][hapmap];0.81[JPT][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10738356	0.81[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs10810104	0.82[EUR][1000 genomes]
rs10810106	1.00[CEU][hapmap];0.81[CHB][hapmap];0.83[JPT][hapmap];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10810110	0.82[CHB][hapmap];0.93[YRI][hapmap];0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10810113	0.90[CHB][hapmap];0.81[JPT][hapmap];0.87[ASN][1000 genomes]
rs10810114	0.86[CHB][hapmap];0.83[JPT][hapmap];0.88[ASN][1000 genomes]
rs10961400	0.85[CHB][hapmap]
rs10961413	1.00[CEU][hapmap];0.81[JPT][hapmap];0.94[EUR][1000 genomes]
rs10961414	0.92[CEU][hapmap];0.84[EUR][1000 genomes]
rs10961420	0.87[CHB][hapmap];0.83[ASN][1000 genomes]
rs12235129	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12377502	0.85[CHB][hapmap]
rs13287487	0.91[CEU][hapmap]
rs2382448	0.84[CEU][hapmap]
rs2382450	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs2382451	0.92[CEU][hapmap]
rs2382454	1.00[CEU][hapmap];0.90[CHB][hapmap];0.81[JPT][hapmap];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2382456	0.91[CEU][hapmap];0.90[CHB][hapmap];0.81[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2382457	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2382458	0.92[CEU][hapmap];0.82[CHB][hapmap];0.82[JPT][hapmap];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2382459	1.00[CEU][hapmap];0.81[CHB][hapmap];0.91[EUR][1000 genomes]
rs2890982	0.81[CEU][hapmap]
rs2890985	1.00[CEU][hapmap];0.93[YRI][hapmap];0.83[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs4532695	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4551459	0.92[CEU][hapmap]
rs4628344	0.92[CEU][hapmap];0.89[EUR][1000 genomes]
rs6474823	1.00[CEU][hapmap];0.90[CHB][hapmap];0.83[JPT][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6474824	1.00[CEU][hapmap];0.90[CHB][hapmap];0.81[JPT][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6474825	1.00[CEU][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7034162	0.92[CEU][hapmap];0.88[EUR][1000 genomes]
rs73413827	0.94[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:73 , 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	chr9:14188200-14199000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
3	chr9:14190600-14198800	Weak transcription	A549	lung
4	chr9:14191800-14202800	Enhancers	Fetal Heart	heart
5	chr9:14192800-14198800	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr9:14192800-14207400	Weak transcription	Spleen	Spleen
7	chr9:14192800-14213400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr9:14193800-14203000	Enhancers	Fetal Brain Female	brain
9	chr9:14194600-14199000	Enhancers	HUVEC	blood vessel
10	chr9:14196000-14199000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr9:14196000-14205400	Enhancers	Fetal Lung	lung
12	chr9:14196600-14198800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr9:14197000-14201400	Enhancers	Duodenum Smooth Muscle	Duodenum
14	chr9:14197000-14201400	Enhancers	HMEC	breast
15	chr9:14197200-14199800	Enhancers	Fetal Brain Male	brain
16	chr9:14197600-14200200	Enhancers	Fetal Muscle Leg	muscle
17	chr9:14197600-14202800	Weak transcription	Rectal Mucosa Donor 31	rectum
18	chr9:14197800-14198800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr9:14197800-14199400	Enhancers	Duodenum Mucosa	Duodenum
20	chr9:14197800-14199400	Enhancers	HSMM	muscle
21	chr9:14197800-14199600	Enhancers	NH-A	brain
22	chr9:14197800-14200200	Enhancers	NHDF-Ad	bronchial
23	chr9:14197800-14201600	Enhancers	Right Ventricle	heart
24	chr9:14198000-14199000	Enhancers	Muscle Satellite Cultured Cells	--
25	chr9:14198000-14199000	Enhancers	Brain Anterior Caudate	brain
26	chr9:14198000-14199000	Weak transcription	Stomach Mucosa	stomach
27	chr9:14198000-14199400	Enhancers	Sigmoid Colon	Sigmoid Colon
28	chr9:14198000-14199800	Enhancers	Brain Germinal Matrix	brain
29	chr9:14198000-14201400	Enhancers	Cortex derived primary cultured neurospheres	brain
30	chr9:14198200-14199600	Enhancers	Colonic Mucosa	Colon
31	chr9:14198200-14201200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr9:14198200-14204000	Enhancers	Colon Smooth Muscle	Colon
33	chr9:14198400-14198800	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr9:14198400-14199000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr9:14198400-14199200	Enhancers	HSMMtube	muscle
36	chr9:14198400-14199600	Enhancers	Brain Hippocampus Middle	brain
37	chr9:14198400-14200000	Enhancers	Brain Inferior Temporal Lobe	brain
38	chr9:14198400-14200000	Enhancers	Brain Substantia Nigra	brain
39	chr9:14198400-14200200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr9:14198400-14200200	Enhancers	Liver	Liver
41	chr9:14198400-14200400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr9:14198400-14200600	Enhancers	NHEK	skin
43	chr9:14198600-14198800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
44	chr9:14198600-14198800	Flanking Active TSS	Rectal Smooth Muscle	rectum
45	chr9:14198600-14199000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr9:14198600-14199200	Enhancers	ES-I3 Cell Line	embryonic stem cell
47	chr9:14198600-14199200	Flanking Active TSS	Adipose Nuclei	Adipose
48	chr9:14198600-14199200	Enhancers	NHLF	lung
49	chr9:14198600-14199400	Enhancers	Aorta	Aorta
50	chr9:14198600-14199400	Enhancers	Brain Cingulate Gyrus	brain

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