Variant report

Variant	rs7649428
Chromosome Location	chr3:49868876-49868877
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAX	chr3:49868876-49869009	NB4	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:49868258..49870726-chr3:49875170..49876844,2	MCF-7	breast:

Variant related genes	Relation type
TRAIP	TF binding region

Extended variants
information (count: 61 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs11130217	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11709734	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11720705	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12715437	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13091525	1.00[ASN][1000 genomes]
rs13095697	1.00[ASN][1000 genomes]
rs13097720	1.00[ASN][1000 genomes]
rs1491985	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17225749	1.00[ASN][1000 genomes]
rs17304079	1.00[ASN][1000 genomes]
rs1799844	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1996663	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1996664	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs28535523	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3020779	0.81[EUR][1000 genomes]
rs35012435	1.00[ASN][1000 genomes]
rs35129566	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35375092	1.00[ASN][1000 genomes]
rs35491931	1.00[ASN][1000 genomes]
rs35849525	1.00[ASN][1000 genomes]
rs55924524	1.00[ASN][1000 genomes]
rs55997059	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs58339610	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59357103	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs59684465	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs61557789	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs62260663	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62260720	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62260723	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs62260755	1.00[ASN][1000 genomes]
rs62262061	1.00[ASN][1000 genomes]
rs62262106	1.00[ASN][1000 genomes]
rs62262118	1.00[ASN][1000 genomes]
rs62262722	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62262730	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62263602	1.00[ASN][1000 genomes]
rs6787892	1.00[ASN][1000 genomes]
rs6790568	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6804970	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6809879	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs71326904	1.00[ASN][1000 genomes]
rs71326915	1.00[ASN][1000 genomes]
rs7613603	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7615318	1.00[ASN][1000 genomes]
rs7620848	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7621797	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7628207	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7635601	1.00[ASN][1000 genomes]
rs7637711	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7648652	1.00[ASN][1000 genomes]
rs9829155	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9835157	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9836756	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9851651	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9870755	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9870858	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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
5	nsv967270	chr3:49845381-49870409	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7649428	AMT	cis	lung	GTEx
rs7649428	AMT	cis	Thyroid	GTEx

Chromatin state (count:96 , 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	chr3:49865000-49869800	Strong transcription	Primary neutrophils fromperipheralblood	blood
25	chr3:49865000-49870800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
26	chr3:49865000-49872400	Strong transcription	Fetal Muscle Leg	muscle
27	chr3:49865000-49872800	Strong transcription	Fetal Stomach	stomach
28	chr3:49865000-49876400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr3:49865000-49876400	Strong transcription	HUES64 Cell Line	embryonic stem cell
30	chr3:49865000-49886000	Strong transcription	Dnd41	blood
31	chr3:49865200-49869000	Weak transcription	Muscle Satellite Cultured Cells	--
32	chr3:49865200-49872000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr3:49865200-49872200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr3:49865200-49872400	Strong transcription	H9 Cell Line	embryonic stem cell
35	chr3:49865200-49872800	Strong transcription	Fetal Intestine Small	intestine
36	chr3:49865200-49876200	Strong transcription	Cortex derived primary cultured neurospheres	brain
37	chr3:49865200-49877000	Weak transcription	Right Ventricle	heart
38	chr3:49865200-49877400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr3:49865400-49870000	Weak transcription	HSMM	muscle
40	chr3:49865600-49869200	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr3:49865600-49869200	Strong transcription	Brain Germinal Matrix	brain
42	chr3:49865600-49869600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
43	chr3:49865600-49869600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
44	chr3:49865600-49869800	Strong transcription	H1 Cell Line	embryonic stem cell
45	chr3:49865600-49876000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr3:49865600-49876800	Weak transcription	Rectal Smooth Muscle	rectum
47	chr3:49865600-49885800	Strong transcription	HUES48 Cell Line	embryonic stem cell
48	chr3:49865600-49885800	Strong transcription	HUES6 Cell Line	embryonic stem cell
49	chr3:49865800-49869200	Strong transcription	Esophagus	oesophagus
50	chr3:49865800-49869400	Strong transcription	Primary T cells from cord blood	blood

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