Variant report

Variant	rs62260723
Chromosome Location	chr3:49872124-49872125
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:49870527..49872385-chr3:49950904..49952666,2	MCF-7	breast:
2	chr3:49850294..49853000-chr3:49870481..49872389,2	K562	blood:

Variant related genes	Relation type
ENSG00000182179	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs11130217	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11709734	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11720705	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12715437	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1491985	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1799844	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1996663	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1996664	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28535523	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3020779	0.81[EUR][1000 genomes]
rs35129566	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55997059	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58339610	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs59357103	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs59684465	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61557789	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62260663	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62260720	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62262722	0.95[EUR][1000 genomes]
rs62262730	0.96[EUR][1000 genomes]
rs6790568	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6804970	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6809879	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7613603	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7620848	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7621797	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7628207	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7637711	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7649428	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9829155	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9835157	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9836756	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9851651	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9870755	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9870858	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1796352	chr3:49687101-49949959	Genic enhancers Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
2	nsv834688	chr3:49811115-50019299	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
3	esv1809827	chr3:49812331-49934179	Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
4	nsv876766	chr3:49817450-49961780	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs62260723	AMT	cis	lung	GTEx
rs62260723	AMT	cis	Thyroid	GTEx

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49861200-49882200	Weak transcription	Primary B cells from cord blood	blood
2	chr3:49861200-49893200	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr3:49863400-49876800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr3:49863400-49876800	Weak transcription	Brain Substantia Nigra	brain
5	chr3:49863400-49879000	Weak transcription	Fetal Brain Male	brain
6	chr3:49863600-49876600	Weak transcription	Brain Hippocampus Middle	brain
7	chr3:49863800-49874000	Weak transcription	Primary hematopoietic stem cells	blood
8	chr3:49863800-49875600	Weak transcription	Skeletal Muscle Male	skeletal muscle
9	chr3:49863800-49879000	Weak transcription	NH-A	brain
10	chr3:49863800-49882800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
11	chr3:49864000-49876600	Weak transcription	Primary T cells fromperipheralblood	blood
12	chr3:49864000-49883200	Weak transcription	Colonic Mucosa	Colon
13	chr3:49864000-49893200	Weak transcription	Placenta	Placenta
14	chr3:49864200-49873000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
15	chr3:49864200-49876800	Weak transcription	Rectal Mucosa Donor 31	rectum
16	chr3:49864200-49893000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr3:49864400-49876800	Weak transcription	Brain Anterior Caudate	brain
18	chr3:49864600-49876800	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr3:49864600-49882000	Weak transcription	Osteobl	bone
20	chr3:49864800-49872800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr3:49864800-49878000	Strong transcription	Fetal Thymus	thymus
22	chr3:49864800-49880400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr3:49864800-49886000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr3:49865000-49872400	Strong transcription	Fetal Muscle Leg	muscle
25	chr3:49865000-49872800	Strong transcription	Fetal Stomach	stomach
26	chr3:49865000-49876400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr3:49865000-49876400	Strong transcription	HUES64 Cell Line	embryonic stem cell
28	chr3:49865000-49886000	Strong transcription	Dnd41	blood
29	chr3:49865200-49872200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr3:49865200-49872400	Strong transcription	H9 Cell Line	embryonic stem cell
31	chr3:49865200-49872800	Strong transcription	Fetal Intestine Small	intestine
32	chr3:49865200-49876200	Strong transcription	Cortex derived primary cultured neurospheres	brain
33	chr3:49865200-49877000	Weak transcription	Right Ventricle	heart
34	chr3:49865200-49877400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr3:49865600-49876000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr3:49865600-49876800	Weak transcription	Rectal Smooth Muscle	rectum
37	chr3:49865600-49885800	Strong transcription	HUES48 Cell Line	embryonic stem cell
38	chr3:49865600-49885800	Strong transcription	HUES6 Cell Line	embryonic stem cell
39	chr3:49866000-49881000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr3:49866200-49872200	Strong transcription	Thymus	Thymus
41	chr3:49866200-49872400	Strong transcription	Fetal Muscle Trunk	muscle
42	chr3:49866200-49872400	Strong transcription	Monocytes-CD14+_RO01746	blood
43	chr3:49866200-49876800	Weak transcription	HUVEC	blood vessel
44	chr3:49866600-49876600	Weak transcription	Primary B cells from peripheral blood	blood
45	chr3:49867000-49876800	Weak transcription	Right Atrium	heart
46	chr3:49867200-49876800	Weak transcription	Ovary	ovary
47	chr3:49867600-49876600	Weak transcription	Fetal Lung	lung
48	chr3:49867800-49879000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr3:49868200-49878600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr3:49869000-49876800	Weak transcription	NHLF	lung

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