Variant report

Variant	rs9854081
Chromosome Location	chr3:120457838-120457839
allele	C/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	CTCF	chr3:120457740-120457890	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:120456023..120459127-chr3:120459888..120461949,3	MCF-7	breast:
2	chr3:120456048..120458212-chr3:120459469..120461688,2	MCF-7	breast:

Variant related genes	Relation type
GTF2E1	TF binding region
ENSG00000144840	Chromatin interaction
ENSG00000153767	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10511404	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11714961	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12489104	0.84[MKK][hapmap];0.85[TSI][hapmap];1.00[YRI][hapmap]
rs13316584	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1566988	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs167722	0.86[ASN][1000 genomes]
rs172819	0.83[CHB][hapmap];0.81[JPT][hapmap];0.85[ASN][1000 genomes]
rs178725	0.87[ASN][1000 genomes]
rs2288096	0.84[MKK][hapmap];0.81[TSI][hapmap];1.00[YRI][hapmap]
rs2292719	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs373188	0.87[ASN][1000 genomes]
rs417061	0.83[CHB][hapmap];0.81[JPT][hapmap];0.87[ASN][1000 genomes]
rs4501055	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs519336	0.83[CHB][hapmap];0.93[CHD][hapmap];0.81[JPT][hapmap];0.86[ASN][1000 genomes]
rs55831173	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56406902	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs607953	0.83[CHB][hapmap];0.93[CHD][hapmap];0.81[JPT][hapmap];0.87[ASN][1000 genomes]
rs618642	0.83[CHB][hapmap];0.93[CHD][hapmap];0.81[JPT][hapmap];0.86[ASN][1000 genomes]
rs6778859	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6796222	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73183726	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7430785	1.00[YRI][hapmap]
rs7620570	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7633399	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9814744	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9838458	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9872831	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9985346	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1007557	chr3:119892894-120764353	Enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
2	nsv536706	chr3:119892894-120764353	Flanking Bivalent TSS/Enh Enhancers Active TSS Weak transcription Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	nsv829699	chr3:120308332-120484695	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	19 gene(s)	inside rSNPs	diseases
4	nsv869548	chr3:120320731-121076337	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
5	nsv916869	chr3:120360281-120973169	Active TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Enhancers Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
6	nsv877378	chr3:120381530-120606438	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs9854081	UMPS	cis	cerebellum	SCAN
rs9854081	ALDH1L1	cis	parietal	SCAN
rs9854081	SLC41A3	cis	cerebellum	SCAN
rs9854081	STXBP5L	cis	cerebellum	SCAN
rs9854081	FSTL1	cis	parietal	SCAN

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:120416400-120460600	Weak transcription	Brain Inferior Temporal Lobe	brain
2	chr3:120416800-120460600	Weak transcription	Muscle Satellite Cultured Cells	--
3	chr3:120423000-120460200	Weak transcription	HUVEC	blood vessel
4	chr3:120438400-120460200	Weak transcription	NHEK	skin
5	chr3:120438400-120460600	Weak transcription	Brain Anterior Caudate	brain
6	chr3:120438400-120460600	Weak transcription	Right Ventricle	heart
7	chr3:120438600-120460000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
8	chr3:120438600-120460400	Weak transcription	Rectal Smooth Muscle	rectum
9	chr3:120439000-120460200	Weak transcription	Primary B cells from cord blood	blood
10	chr3:120439200-120460200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr3:120439800-120460200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
12	chr3:120441400-120460000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
13	chr3:120442600-120460400	Weak transcription	Brain Substantia Nigra	brain
14	chr3:120443800-120460200	Weak transcription	HSMM	muscle
15	chr3:120445000-120460600	Weak transcription	Brain Cingulate Gyrus	brain
16	chr3:120446800-120460400	Weak transcription	Pancreatic Islets	Pancreatic Islet
17	chr3:120447200-120460200	Weak transcription	Brain Angular Gyrus	brain
18	chr3:120447200-120460600	Weak transcription	Fetal Heart	heart
19	chr3:120447600-120460200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr3:120447600-120460200	Weak transcription	Duodenum Smooth Muscle	Duodenum
21	chr3:120448200-120460200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr3:120448200-120460200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr3:120448200-120460200	Weak transcription	Primary B cells from peripheral blood	blood
24	chr3:120448200-120460200	Weak transcription	Colon Smooth Muscle	Colon
25	chr3:120448400-120460200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr3:120449800-120460200	Weak transcription	Adipose Nuclei	Adipose
27	chr3:120450600-120460200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr3:120455000-120459600	Weak transcription	Dnd41	blood
29	chr3:120455000-120460400	Weak transcription	Primary neutrophils fromperipheralblood	blood
30	chr3:120455200-120460600	Weak transcription	Placenta Amnion	Placenta Amnion
31	chr3:120455800-120458200	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr3:120456000-120458000	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
33	chr3:120456200-120458000	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
34	chr3:120456200-120458000	ZNF genes & repeats	Fetal Stomach	stomach
35	chr3:120456400-120458000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr3:120456400-120458000	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr3:120456400-120458000	Strong transcription	Duodenum Mucosa	Duodenum
38	chr3:120456400-120458000	ZNF genes & repeats	Fetal Muscle Leg	muscle
39	chr3:120456400-120458800	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
40	chr3:120456600-120458000	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr3:120456600-120458000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
42	chr3:120456800-120458800	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
43	chr3:120456800-120460000	Weak transcription	Primary T cells from cord blood	blood
44	chr3:120456800-120460200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
45	chr3:120456800-120460200	Weak transcription	HMEC	breast
46	chr3:120456800-120460600	Weak transcription	Brain Hippocampus Middle	brain
47	chr3:120457000-120460200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
48	chr3:120457200-120458000	Strong transcription	Fetal Muscle Trunk	muscle
49	chr3:120457200-120460000	Weak transcription	Primary T helper cells fromperipheralblood	blood
50	chr3:120457400-120458000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links