Variant report

Variant	rs530456
Chromosome Location	chr9:116381932-116381933
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:116172702..116174409-chr9:116381360..116383255,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000157653	Chromatin interaction
ENSG00000148229	Chromatin interaction

Extended variants
information (count: 75 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:62)

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]
rs1547694	1.00[YRI][hapmap];0.95[AFR][1000 genomes]
rs16907354	1.00[ASN][1000 genomes]
rs17766289	1.00[ASN][1000 genomes]
rs2039225	0.87[EUR][1000 genomes]
rs2812400	0.95[AFR][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];0.95[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs485184	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs502942	0.95[AFR][1000 genomes]
rs505668	1.00[YRI][hapmap];0.95[AFR][1000 genomes]
rs511561	1.00[ASN][1000 genomes]
rs538711	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs551960	0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55916010	1.00[ASN][1000 genomes]
rs56038206	1.00[ASN][1000 genomes]
rs565016	0.87[EUR][1000 genomes]
rs57989349	1.00[ASN][1000 genomes]
rs586265	1.00[CEU][hapmap];0.95[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60302610	1.00[ASN][1000 genomes]
rs608290	1.00[CEU][hapmap];0.89[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs611335	1.00[CEU][hapmap];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs641266	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6478012	1.00[ASN][1000 genomes]
rs6478017	1.00[ASN][1000 genomes]
rs653971	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs664850	0.94[CEU][hapmap];0.95[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs670719	0.89[AMR][1000 genomes];0.93[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:13 , 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	nsv893747	chr9:116214058-116386438	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
3	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
4	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
5	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
6	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
7	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
8	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
9	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
10	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
11	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
12	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
13	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:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:116373600-116382400	Weak transcription	HUES48 Cell Line	embryonic stem cell
2	chr9:116375600-116382400	Enhancers	Breast Myoepithelial Primary Cells	Breast
3	chr9:116376200-116386000	Enhancers	Cortex derived primary cultured neurospheres	brain
4	chr9:116376800-116382200	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr9:116377000-116382200	Enhancers	Primary B cells from cord blood	blood
6	chr9:116377000-116382800	Enhancers	Primary B cells from peripheral blood	blood
7	chr9:116377400-116382200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr9:116377400-116382400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr9:116377800-116382200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr9:116377800-116382200	Weak transcription	Duodenum Smooth Muscle	Duodenum
11	chr9:116377800-116382400	Weak transcription	Rectal Smooth Muscle	rectum
12	chr9:116378000-116382400	Weak transcription	Brain Angular Gyrus	brain
13	chr9:116378200-116382200	Weak transcription	Brain Hippocampus Middle	brain
14	chr9:116378600-116382000	Weak transcription	Brain Anterior Caudate	brain
15	chr9:116378600-116382000	Weak transcription	Fetal Intestine Large	intestine
16	chr9:116378600-116382200	Weak transcription	Aorta	Aorta
17	chr9:116378600-116382600	Weak transcription	Psoas Muscle	Psoas
18	chr9:116378800-116382400	Weak transcription	Esophagus	oesophagus
19	chr9:116379000-116382000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr9:116379000-116382000	Weak transcription	Muscle Satellite Cultured Cells	--
21	chr9:116379000-116382400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr9:116379000-116382600	Weak transcription	Brain Cingulate Gyrus	brain
23	chr9:116379400-116382000	Weak transcription	Left Ventricle	heart
24	chr9:116379400-116383000	Weak transcription	Brain Substantia Nigra	brain
25	chr9:116379800-116382200	Weak transcription	H1 Cell Line	embryonic stem cell
26	chr9:116380000-116382000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr9:116380000-116382000	Weak transcription	Sigmoid Colon	Sigmoid Colon
28	chr9:116380000-116382400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr9:116380200-116382000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr9:116380200-116382200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
31	chr9:116380200-116382200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr9:116380200-116382200	Weak transcription	HUES64 Cell Line	embryonic stem cell
33	chr9:116380200-116382200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
34	chr9:116380200-116382200	Weak transcription	Fetal Lung	lung
35	chr9:116380200-116382400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr9:116380200-116382400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
37	chr9:116380200-116382600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr9:116380200-116382800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
39	chr9:116380400-116382000	Weak transcription	NHEK	skin
40	chr9:116380600-116382600	Enhancers	Fetal Muscle Trunk	muscle
41	chr9:116380600-116384200	Enhancers	Spleen	Spleen
42	chr9:116380800-116382000	Enhancers	Fetal Heart	heart
43	chr9:116380800-116382200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
44	chr9:116381000-116382600	Enhancers	Adipose Nuclei	Adipose
45	chr9:116381200-116382400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr9:116381200-116382400	Enhancers	NHDF-Ad	bronchial
47	chr9:116381200-116382600	Enhancers	Primary hematopoietic stem cells short term culture	blood
48	chr9:116381200-116382600	Enhancers	Stomach Smooth Muscle	stomach
49	chr9:116381200-116384200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr9:116381200-116384200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived

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