Variant report

Variant	rs6550826
Chromosome Location	chr3:24034988-24034989
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:23988282..23990131-chr3:24033697..24035885,2	MCF-7	breast:
2	chr3:24033657..24035811-chr3:24038955..24040843,2	MCF-7	breast:
3	chr3:24033672..24036269-chr3:24038559..24040609,2	K562	blood:

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10865791	0.86[CHB][hapmap]
rs11129130	0.86[CHB][hapmap]
rs13095392	0.82[JPT][hapmap]
rs1533140	0.83[CEU][hapmap];0.89[YRI][hapmap];0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1567582	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs36083758	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4078155	0.83[CHB][hapmap]
rs4241522	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4292186	0.83[CHB][hapmap]
rs4293661	0.83[CHB][hapmap]
rs4578971	0.86[CHB][hapmap]
rs4589882	0.81[JPT][hapmap]
rs4858561	0.86[CHB][hapmap]
rs6550823	0.81[JPT][hapmap]
rs6550825	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6550828	0.95[CHB][hapmap];0.95[JPT][hapmap];0.99[ASN][1000 genomes]
rs6779476	0.91[CHB][hapmap];0.85[JPT][hapmap];0.87[ASN][1000 genomes]
rs6800790	0.88[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.92[YRI][hapmap];0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7610892	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7610993	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7619870	0.84[ASN][1000 genomes]
rs7631236	0.80[ASN][1000 genomes]
rs7646930	0.86[CHB][hapmap]
rs9831760	0.83[CHB][hapmap]
rs9883101	0.93[YRI][hapmap];0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv533980	chr3:23445901-24311972	ZNF genes & repeats Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
2	nsv834638	chr3:23963860-24117191	Enhancers Weak transcription Active TSS Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats 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	19 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:24019400-24035400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
2	chr3:24019600-24040800	Weak transcription	NHLF	lung
3	chr3:24023200-24035000	Weak transcription	Right Atrium	heart
4	chr3:24023200-24035200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr3:24024000-24035200	Weak transcription	Left Ventricle	heart
6	chr3:24029000-24035000	Weak transcription	Lung	lung
7	chr3:24030800-24040400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr3:24032200-24035800	Enhancers	Fetal Brain Female	brain
9	chr3:24032200-24036000	Enhancers	Brain Substantia Nigra	brain
10	chr3:24032200-24036200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
11	chr3:24032200-24036600	Enhancers	Fetal Stomach	stomach
12	chr3:24032600-24036000	Enhancers	Fetal Lung	lung
13	chr3:24032600-24036200	Enhancers	Rectal Smooth Muscle	rectum
14	chr3:24032800-24036400	Enhancers	Colon Smooth Muscle	Colon
15	chr3:24032800-24036800	Enhancers	Fetal Heart	heart
16	chr3:24033200-24036000	Enhancers	Psoas Muscle	Psoas
17	chr3:24033200-24036200	Enhancers	Skeletal Muscle Female	skeletal muscle
18	chr3:24033400-24035000	Weak transcription	Fetal Intestine Small	intestine
19	chr3:24033400-24036400	Enhancers	Cortex derived primary cultured neurospheres	brain
20	chr3:24033600-24035000	Weak transcription	Duodenum Smooth Muscle	Duodenum
21	chr3:24033600-24036000	Enhancers	Brain Germinal Matrix	brain
22	chr3:24033600-24039000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr3:24033600-24040600	Weak transcription	Primary B cells from cord blood	blood
24	chr3:24033800-24035000	Weak transcription	Fetal Muscle Leg	muscle
25	chr3:24033800-24036000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr3:24033800-24036200	Enhancers	Brain Cingulate Gyrus	brain
27	chr3:24033800-24036600	Enhancers	Primary hematopoietic stem cells	blood
28	chr3:24033800-24040600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr3:24034000-24035000	Weak transcription	Fetal Thymus	thymus
30	chr3:24034000-24035200	Weak transcription	Stomach Mucosa	stomach
31	chr3:24034000-24036200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr3:24034200-24035200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr3:24034200-24035200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr3:24034200-24035200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr3:24034200-24035200	Enhancers	Brain Anterior Caudate	brain
36	chr3:24034200-24035200	Weak transcription	HSMMtube	muscle
37	chr3:24034200-24035400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr3:24034200-24035400	Weak transcription	Adipose Nuclei	Adipose
39	chr3:24034200-24035400	Weak transcription	Fetal Kidney	kidney
40	chr3:24034200-24035400	Weak transcription	NHDF-Ad	bronchial
41	chr3:24034200-24035800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr3:24034200-24035800	Enhancers	Brain Angular Gyrus	brain
43	chr3:24034200-24036000	Enhancers	Brain Hippocampus Middle	brain
44	chr3:24034200-24036000	Enhancers	Brain Inferior Temporal Lobe	brain
45	chr3:24034200-24036200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr3:24034200-24036800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr3:24034200-24039000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr3:24034400-24036000	Enhancers	Fetal Brain Male	brain
49	chr3:24034600-24035000	Weak transcription	Stomach Smooth Muscle	stomach
50	chr3:24034600-24036400	Enhancers	Aorta	Aorta

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