Variant report

Variant	rs653971
Chromosome Location	chr9:116387389-116387390
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:116385601..116388209-chr9:116407553..116409087,2	MCF-7	breast:
2	chr9:116385537..116387562-chr9:116409870..116412944,3	MCF-7	breast:
3	chr9:116378512..116381632-chr9:116384610..116387755,3	MCF-7	breast:
4	chr9:116382263..116386126-chr9:116386783..116389124,3	MCF-7	breast:
5	chr9:116386561..116388140-chr9:116399851..116401503,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000233817	Chromatin interaction

Extended variants
information (count: 70 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs10217237	1.00[ASN][1000 genomes]
rs10217750	1.00[ASN][1000 genomes]
rs10217756	1.00[ASN][1000 genomes]
rs10481640	1.00[ASN][1000 genomes]
rs10817496	1.00[ASN][1000 genomes]
rs10981794	1.00[ASN][1000 genomes]
rs10981840	1.00[ASN][1000 genomes]
rs10981841	1.00[ASN][1000 genomes]
rs10981843	1.00[ASN][1000 genomes]
rs10981844	1.00[ASN][1000 genomes]
rs10981845	1.00[ASN][1000 genomes]
rs10981846	1.00[ASN][1000 genomes]
rs10981847	1.00[ASN][1000 genomes]
rs10981850	1.00[ASN][1000 genomes]
rs12335991	1.00[ASN][1000 genomes]
rs12336983	1.00[ASN][1000 genomes]
rs12338221	1.00[ASN][1000 genomes]
rs12339851	1.00[ASN][1000 genomes]
rs12344964	1.00[ASN][1000 genomes]
rs16907354	1.00[ASN][1000 genomes]
rs17766289	1.00[ASN][1000 genomes]
rs2039225	0.80[EUR][1000 genomes]
rs28709996	1.00[ASN][1000 genomes]
rs36062487	1.00[ASN][1000 genomes]
rs41276817	1.00[ASN][1000 genomes]
rs41297197	1.00[ASN][1000 genomes]
rs4348575	1.00[ASN][1000 genomes]
rs4609260	1.00[ASN][1000 genomes]
rs483284	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs485184	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs511561	1.00[ASN][1000 genomes]
rs530456	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs538711	1.00[CEU][hapmap];0.97[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs551960	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55916010	1.00[ASN][1000 genomes]
rs56038206	1.00[ASN][1000 genomes]
rs565016	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs57989349	1.00[ASN][1000 genomes]
rs586265	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60302610	1.00[ASN][1000 genomes]
rs608290	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs611335	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs641266	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6478012	1.00[ASN][1000 genomes]
rs6478017	1.00[ASN][1000 genomes]
rs664850	0.94[CEU][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs670719	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7021491	1.00[ASN][1000 genomes]
rs7033679	1.00[ASN][1000 genomes]
rs72761905	1.00[ASN][1000 genomes]
rs72761964	1.00[ASN][1000 genomes]
rs72761969	1.00[ASN][1000 genomes]
rs72761971	1.00[ASN][1000 genomes]
rs72761973	1.00[ASN][1000 genomes]
rs72761978	1.00[ASN][1000 genomes]
rs72761995	1.00[ASN][1000 genomes]
rs7867203	1.00[ASN][1000 genomes]
rs7870265	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530949	chr9:115821128-116487796	Flanking Active TSS Enhancers Active TSS Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
2	nsv526579	chr9:116244982-116391162	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
3	nsv893748	chr9:116308709-116421786	Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
4	nsv430093	chr9:116330446-117325446	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	165 gene(s)	inside rSNPs	diseases
5	nsv466509	chr9:116356516-116396098	Weak transcription Enhancers Genic enhancers Bivalent Enhancer Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' 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
6	nsv615216	chr9:116356516-116396098	Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
7	nsv466510	chr9:116363877-116397397	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
8	nsv615217	chr9:116363877-116397397	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
9	nsv615218	chr9:116365126-116391069	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
10	nsv466511	chr9:116374990-116397397	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
11	nsv615219	chr9:116374990-116397397	Bivalent Enhancer Flanking Active TSS Weak transcription Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Genic enhancers	TF binding region Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
12	nsv893749	chr9:116378759-116439749	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:116382600-116387800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr9:116382800-116387400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr9:116383600-116387600	Weak transcription	Aorta	Aorta
4	chr9:116383600-116387800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr9:116383600-116389800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr9:116383800-116387400	Weak transcription	Psoas Muscle	Psoas
7	chr9:116383800-116389000	Weak transcription	Right Atrium	heart
8	chr9:116384000-116389400	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr9:116384200-116388200	Enhancers	Muscle Satellite Cultured Cells	--
10	chr9:116384200-116389000	Weak transcription	Brain Hippocampus Middle	brain
11	chr9:116384200-116389200	Weak transcription	Brain Substantia Nigra	brain
12	chr9:116384200-116396400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr9:116384400-116388600	Weak transcription	Colon Smooth Muscle	Colon
14	chr9:116384400-116389000	Weak transcription	Fetal Lung	lung
15	chr9:116384400-116390400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr9:116384600-116387400	Enhancers	Osteobl	bone
17	chr9:116384600-116389000	Weak transcription	Duodenum Smooth Muscle	Duodenum
18	chr9:116385000-116389800	Enhancers	NHDF-Ad	bronchial
19	chr9:116385000-116396400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr9:116385200-116387800	Enhancers	Right Ventricle	heart
21	chr9:116385400-116388000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr9:116385400-116388000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr9:116385400-116388000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr9:116385600-116389600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr9:116385800-116387600	Weak transcription	Lung	lung
26	chr9:116385800-116388000	Enhancers	NH-A	brain
27	chr9:116385800-116388600	Weak transcription	Rectal Smooth Muscle	rectum
28	chr9:116385800-116388800	Weak transcription	Adipose Nuclei	Adipose
29	chr9:116385800-116389000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
30	chr9:116385800-116394200	Weak transcription	Placenta Amnion	Placenta Amnion
31	chr9:116385800-116402600	Weak transcription	Stomach Mucosa	stomach
32	chr9:116386000-116389200	Weak transcription	HUVEC	blood vessel
33	chr9:116386000-116395200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr9:116386200-116390200	Enhancers	Skeletal Muscle Male	skeletal muscle
35	chr9:116386400-116387400	Weak transcription	HSMMtube	muscle
36	chr9:116386400-116389200	Weak transcription	HUES6 Cell Line	embryonic stem cell
37	chr9:116386600-116387600	Weak transcription	Left Ventricle	heart
38	chr9:116386600-116390000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr9:116387000-116387600	Enhancers	Fetal Muscle Trunk	muscle
40	chr9:116387000-116387800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr9:116387000-116388000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr9:116387000-116388000	Enhancers	NHLF	lung
43	chr9:116387200-116387400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr9:116387200-116387400	Flanking Active TSS	Stomach Smooth Muscle	stomach
45	chr9:116387200-116387600	Enhancers	Cortex derived primary cultured neurospheres	brain
46	chr9:116387200-116387600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr9:116387200-116387600	Flanking Active TSS	Fetal Heart	heart
48	chr9:116387200-116387600	Enhancers	Skeletal Muscle Female	skeletal muscle
49	chr9:116387200-116387600	Enhancers	HMEC	breast
50	chr9:116387200-116387800	Enhancers	Placenta	Placenta

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