Variant report

Variant	rs11580689
Chromosome Location	chr1:223906640-223906641
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	chr1:223906267..223909049-chr1:223925924..223927616,2	MCF-7	breast:
2	chr1:223885961..223896993-chr1:223898177..223910405,32	MCF-7	breast:

Variant related genes	Relation type
ENSG00000162909	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10916601	0.82[ASN][1000 genomes]
rs10916602	0.82[ASN][1000 genomes]
rs11579787	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11581716	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11588475	0.90[EUR][1000 genomes]
rs12057708	0.81[AMR][1000 genomes]
rs12074091	0.82[ASN][1000 genomes]
rs12080565	1.00[CEU][hapmap];0.86[CHB][hapmap];0.89[JPT][hapmap];0.91[YRI][hapmap];0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1539707	0.91[ASN][1000 genomes]
rs16842040	1.00[CEU][hapmap];0.86[CHB][hapmap];0.94[JPT][hapmap];0.91[YRI][hapmap];0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs16842062	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1892077	0.80[CHB][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs2154113	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2186006	0.94[JPT][hapmap];0.82[ASN][1000 genomes]
rs2275877	0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs28370012	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs28370013	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs28370014	0.82[ASN][1000 genomes]
rs28370020	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28370029	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4653499	0.82[ASN][1000 genomes]
rs61823966	0.82[ASN][1000 genomes]
rs6669046	0.91[CHB][hapmap];0.90[JPT][hapmap];0.96[ASN][1000 genomes]
rs6674733	0.95[ASN][1000 genomes]
rs7366009	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs7414311	0.82[ASN][1000 genomes]
rs7543197	0.80[CHB][hapmap];0.95[JPT][hapmap]
rs7555491	0.94[JPT][hapmap];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832681	chr1:223698048-224002691	Strong transcription Active TSS Enhancers Genic enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	esv3361888	chr1:223725597-224114846	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv1007380	chr1:223834380-224042190	Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	nsv535310	chr1:223834380-224042190	ZNF genes & repeats Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
5	esv34082	chr1:223851018-224144509	Enhancers Genic enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
6	nsv873213	chr1:223885843-223924236	Enhancers Bivalent Enhancer Genic enhancers Flanking Active TSS Strong transcription Weak transcription Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	20 gene(s)	inside rSNPs	diseases
7	nsv1008800	chr1:223904653-224061032	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers 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

No data

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:223901400-223907600	Transcr. at gene 5' and 3'	A549	lung
2	chr1:223902200-223913400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr1:223902800-223914200	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr1:223903000-223907800	Weak transcription	Liver	Liver
5	chr1:223903200-223907200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr1:223903200-223913600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr1:223903400-223907400	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
8	chr1:223903400-223908400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr1:223903400-223908800	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr1:223903600-223909400	Strong transcription	Cortex derived primary cultured neurospheres	brain
11	chr1:223903600-223911800	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr1:223903600-223922400	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr1:223904000-223909000	Genic enhancers	Hela-S3	cervix
14	chr1:223904000-223910000	Genic enhancers	Osteobl	bone
15	chr1:223904200-223906800	Strong transcription	Fetal Lung	lung
16	chr1:223904200-223909800	Genic enhancers	NH-A	brain
17	chr1:223904400-223907400	Genic enhancers	HMEC	breast
18	chr1:223904400-223910000	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr1:223904400-223913000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr1:223904400-223922400	Genic enhancers	NHLF	lung
21	chr1:223904600-223907200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
22	chr1:223904600-223907600	Weak transcription	Small Intestine	intestine
23	chr1:223904600-223908000	Weak transcription	Thymus	Thymus
24	chr1:223904600-223908600	Weak transcription	Rectal Smooth Muscle	rectum
25	chr1:223904600-223908600	Weak transcription	Right Atrium	heart
26	chr1:223904600-223909800	Genic enhancers	HUVEC	blood vessel
27	chr1:223904600-223913600	Strong transcription	Brain Anterior Caudate	brain
28	chr1:223904600-223914000	Genic enhancers	NHDF-Ad	bronchial
29	chr1:223904800-223907400	Strong transcription	K562	blood
30	chr1:223904800-223908000	Genic enhancers	Placenta	Placenta
31	chr1:223904800-223908400	Strong transcription	Skeletal Muscle Male	skeletal muscle
32	chr1:223904800-223909000	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr1:223904800-223909000	Strong transcription	Brain Angular Gyrus	brain
34	chr1:223904800-223909200	Strong transcription	Brain Cingulate Gyrus	brain
35	chr1:223904800-223909400	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
36	chr1:223904800-223909400	Strong transcription	Brain Inferior Temporal Lobe	brain
37	chr1:223904800-223909600	Genic enhancers	HSMM	muscle
38	chr1:223904800-223910600	Genic enhancers	Muscle Satellite Cultured Cells	--
39	chr1:223904800-223911800	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr1:223904800-223913200	Strong transcription	Fetal Stomach	stomach
41	chr1:223904800-223914000	Genic enhancers	Primary T cells fromperipheralblood	blood
42	chr1:223905000-223906800	Genic enhancers	Colonic Mucosa	Colon
43	chr1:223905000-223906800	Genic enhancers	Sigmoid Colon	Sigmoid Colon
44	chr1:223905000-223906800	Strong transcription	Stomach Mucosa	stomach
45	chr1:223905000-223907000	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
46	chr1:223905000-223907000	Genic enhancers	Rectal Mucosa Donor 29	rectum
47	chr1:223905000-223907400	Genic enhancers	Rectal Mucosa Donor 31	rectum
48	chr1:223905000-223908400	Strong transcription	Brain Substantia Nigra	brain
49	chr1:223905000-223908400	Strong transcription	Colon Smooth Muscle	Colon
50	chr1:223905000-223909200	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain

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