Variant report

Variant	rs9851651
Chromosome Location	chr3:49825326-49825327
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:1 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:49824989-49825774	HepG2	liver:	n/a	n/a

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:49823748..49825794-chr3:49847684..49850638,2	MCF-7	breast:
2	chr3:49823173..49825666-chr3:49976602..49979269,2	MCF-7	breast:
3	chr3:49824316..49827108-chr3:49830992..49833556,2	MCF-7	breast:
4	chr3:49822915..49825593-chr3:49837367..49840860,3	K562	blood:
5	chr3:49823360..49825533-chr3:49829007..49831424,3	K562	blood:
6	chr3:49759986..49763114-chr3:49822374..49825754,4	MCF-7	breast:
7	chr3:49822569..49826385-chr3:49827149..49830694,4	MCF-7	breast:
8	chr3:49824267..49826162-chr3:49839043..49840811,2	MCF-7	breast:

No data

Variant related genes	Relation type
IP6K1	TF binding region
ENSG00000004534	Chromatin interaction
ENSG00000185614	Chromatin interaction
ENSG00000173540	Chromatin interaction
ENSG00000187492	Chromatin interaction
ENSG00000182179	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs11130217	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11709734	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11720705	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12715437	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13091525	1.00[ASN][1000 genomes]
rs13097720	1.00[ASN][1000 genomes]
rs1491985	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17304079	1.00[ASN][1000 genomes]
rs1799844	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1996663	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1996664	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs28535523	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3020779	0.81[EUR][1000 genomes]
rs35012435	1.00[ASN][1000 genomes]
rs35129566	0.95[AMR][1000 genomes];1.00[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]
rs55997059	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58339610	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59357103	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs59684465	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61557789	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62260663	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62260720	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62260723	0.95[AMR][1000 genomes];1.00[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	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62262730	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6787892	1.00[ASN][1000 genomes]
rs6790568	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6804970	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6809879	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs71326904	1.00[ASN][1000 genomes]
rs71326915	1.00[ASN][1000 genomes]
rs7613603	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7615318	1.00[ASN][1000 genomes]
rs7620848	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7621797	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7628207	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7635601	1.00[ASN][1000 genomes]
rs7637711	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7649428	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9829155	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9835157	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9836756	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9870755	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9870858	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs9851651	AMT	cis	lung	GTEx
rs9851651	AMT	cis	Thyroid	GTEx
rs9851651	RNF123	cis	Artery Tibial	GTEx

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49824600-49825400	Enhancers	Right Atrium	heart
2	chr3:49824600-49825600	Enhancers	Spleen	Spleen
3	chr3:49824600-49827200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr3:49824600-49828200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr3:49824600-49829000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr3:49824600-49832400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr3:49824800-49825400	Enhancers	K562	blood
8	chr3:49824800-49825600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr3:49824800-49825800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr3:49824800-49825800	Enhancers	Brain Cingulate Gyrus	brain
11	chr3:49824800-49827200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr3:49824800-49827200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr3:49824800-49827200	Weak transcription	Brain Hippocampus Middle	brain
14	chr3:49824800-49827200	Weak transcription	Fetal Brain Male	brain
15	chr3:49824800-49827400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr3:49824800-49827400	Weak transcription	Cortex derived primary cultured neurospheres	brain
17	chr3:49824800-49827400	Weak transcription	Brain Substantia Nigra	brain
18	chr3:49824800-49827600	Weak transcription	Fetal Heart	heart
19	chr3:49824800-49827800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr3:49824800-49827800	Weak transcription	Placenta Amnion	Placenta Amnion
21	chr3:49824800-49828200	Weak transcription	NH-A	brain
22	chr3:49824800-49832600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr3:49825000-49826400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr3:49825000-49827200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
25	chr3:49825000-49827200	Weak transcription	Primary B cells from cord blood	blood
26	chr3:49825000-49827200	Weak transcription	Primary T cells from cord blood	blood
27	chr3:49825000-49827200	Weak transcription	Primary T helper cells fromperipheralblood	blood
28	chr3:49825000-49827200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
29	chr3:49825000-49827200	Weak transcription	Thymus	Thymus
30	chr3:49825000-49827400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
31	chr3:49825000-49827400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr3:49825000-49827400	Weak transcription	Fetal Intestine Small	intestine
33	chr3:49825000-49827600	Weak transcription	HUVEC	blood vessel
34	chr3:49825200-49825800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr3:49825200-49827200	Weak transcription	Primary B cells from peripheral blood	blood
36	chr3:49825200-49827200	Weak transcription	Primary hematopoietic stem cells	blood
37	chr3:49825200-49827200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
38	chr3:49825200-49827200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
39	chr3:49825200-49827200	Weak transcription	Fetal Thymus	thymus
40	chr3:49825200-49827200	Weak transcription	Dnd41	blood
41	chr3:49825200-49827200	Weak transcription	HepG2	liver
42	chr3:49825200-49827400	Weak transcription	Primary T helper cells PMA-I stimulated	--
43	chr3:49825200-49827600	Weak transcription	Stomach Mucosa	stomach
44	chr3:49825200-49827800	Weak transcription	HMEC	breast
45	chr3:49825200-49828400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
46	chr3:49825200-49836400	Weak transcription	Esophagus	oesophagus

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links