Variant report

Variant	rs3997
Chromosome Location	chr12:48481587-48481588
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:48479059..48481730-chr12:48499755..48501847,2	K562	blood:
2	chr12:48477502..48480094-chr12:48481006..48483254,2	MCF-7	breast:
3	chr12:48481287..48483908-chr12:48484814..48487764,3	MCF-7	breast:
4	chr12:48480039..48481728-chr12:48497900..48499555,3	K562	blood:
5	chr12:48480039..48481728-chr12:48497655..48499555,3	K562	blood:

Variant related genes	Relation type
ENSG00000079387	Chromatin interaction
ENSG00000152556	Chromatin interaction
ENSG00000226138	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10161358	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10875716	0.88[CEU][hapmap]
rs10875718	0.88[CEU][hapmap]
rs10875719	0.88[CEU][hapmap]
rs10875721	0.80[EUR][1000 genomes]
rs10875743	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10875749	0.92[CEU][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10875753	0.92[CEU][hapmap];0.83[EUR][1000 genomes]
rs11168351	0.88[CEU][hapmap]
rs11168408	1.00[CEU][hapmap];0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11168428	0.92[CEU][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11168437	0.88[CEU][hapmap]
rs12099462	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12228750	1.00[CEU][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12368659	0.92[CEU][hapmap];0.83[EUR][1000 genomes]
rs12816820	0.92[CEU][hapmap];0.83[EUR][1000 genomes]
rs1476607	0.92[CEU][hapmap];0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2051851	1.00[CEU][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4760612	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs4760679	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6580650	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs6580652	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6580654	0.81[EUR][1000 genomes]
rs7139330	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7295580	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7301003	0.92[CEU][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7486941	0.81[CEU][hapmap]
rs7487682	0.81[CEU][hapmap]
rs7971880	0.88[CEU][hapmap]
rs7975632	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8716	0.92[CEU][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs973398	1.00[CEU][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9971924	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][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	esv2758307	chr12:48429702-48825499	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
2	esv2759898	chr12:48429702-48825499	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3997	H1FNT	cis	Muscle Skeletal	GTEx
rs3997	RP1-228P16.1	cis	Artery Tibial	GTEx

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:48432200-48498400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr12:48437200-48489000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr12:48441400-48482600	Weak transcription	Small Intestine	intestine
4	chr12:48453000-48498200	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr12:48454000-48494000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr12:48457400-48482000	Weak transcription	Right Ventricle	heart
7	chr12:48464600-48489400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr12:48464800-48482400	Weak transcription	Rectal Smooth Muscle	rectum
9	chr12:48465000-48487400	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr12:48468400-48482200	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr12:48468400-48482200	Weak transcription	Brain Substantia Nigra	brain
12	chr12:48468600-48498400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr12:48468800-48482800	Weak transcription	Primary hematopoietic stem cells	blood
14	chr12:48468800-48498200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr12:48470200-48497600	Weak transcription	Fetal Heart	heart
16	chr12:48470800-48492800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr12:48471400-48492000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr12:48472200-48489400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr12:48472400-48492000	Strong transcription	Monocytes-CD14+_RO01746	blood
20	chr12:48472600-48486400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr12:48472600-48490200	Strong transcription	Primary T cells fromperipheralblood	blood
22	chr12:48472600-48490200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr12:48472600-48493600	Strong transcription	Fetal Thymus	thymus
24	chr12:48472800-48483200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr12:48472800-48493800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
26	chr12:48473000-48494800	Strong transcription	Primary T helper cells fromperipheralblood	blood
27	chr12:48473200-48482600	Weak transcription	Muscle Satellite Cultured Cells	--
28	chr12:48473200-48486200	Strong transcription	Placenta	Placenta
29	chr12:48473200-48492000	Strong transcription	HUES64 Cell Line	embryonic stem cell
30	chr12:48473600-48490000	Strong transcription	Primary T cells from cord blood	blood
31	chr12:48473600-48495400	Strong transcription	Dnd41	blood
32	chr12:48473800-48491600	Strong transcription	Duodenum Mucosa	Duodenum
33	chr12:48473800-48492800	Strong transcription	Primary T helper cells PMA-I stimulated	--
34	chr12:48474000-48484600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr12:48474000-48485600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr12:48474000-48493000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
37	chr12:48474000-48494800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr12:48474200-48485600	Strong transcription	Primary neutrophils fromperipheralblood	blood
39	chr12:48474200-48486200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
40	chr12:48474600-48492200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr12:48475000-48498200	Weak transcription	Psoas Muscle	Psoas
42	chr12:48475800-48483000	Strong transcription	Hela-S3	cervix
43	chr12:48476000-48483400	Strong transcription	HUES48 Cell Line	embryonic stem cell
44	chr12:48476200-48485800	Strong transcription	HUVEC	blood vessel
45	chr12:48476400-48489400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
46	chr12:48476800-48498400	Weak transcription	Fetal Brain Male	brain
47	chr12:48477000-48484800	Strong transcription	A549	lung
48	chr12:48477200-48498200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
49	chr12:48477400-48482000	Weak transcription	Fetal Lung	lung
50	chr12:48477400-48482200	Weak transcription	Colon Smooth Muscle	Colon

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