Variant report

Variant	rs3314
Chromosome Location	chr1:246931057-246931058
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	GATA3	chr1:246930938-246931493	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:246929352..246931655-chr1:246940972..246943621,2	K562	blood:
2	chr1:246929333..246931322-chr1:246952226..246954934,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000260855	TF binding region
ENSG00000227953	Chromatin interaction
ENSG00000223519	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10924827	0.90[CEU][hapmap];0.97[TSI][hapmap];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11581735	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12023715	0.83[EUR][1000 genomes]
rs12042435	0.84[EUR][1000 genomes]
rs28703972	0.94[EUR][1000 genomes]
rs41267531	0.98[EUR][1000 genomes]
rs56338592	0.84[EUR][1000 genomes]
rs56975801	0.85[EUR][1000 genomes]
rs57384976	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs60107954	0.98[EUR][1000 genomes]
rs6426330	0.82[EUR][1000 genomes]
rs6671220	0.86[EUR][1000 genomes]
rs7414184	0.85[EUR][1000 genomes]
rs7417422	0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949571	chr1:246688635-247240863	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
2	nsv873421	chr1:246818634-247044692	Weak transcription Strong transcription Bivalent/Poised TSS Bivalent Enhancer Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	esv2762192	chr1:246823857-247069232	Weak transcription Strong transcription ZNF genes & repeats Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
4	nsv1006271	chr1:246832606-247276182	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
5	nsv535416	chr1:246832606-247276182	Strong transcription ZNF genes & repeats Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
6	nsv430413	chr1:246845971-246975015	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
7	nsv873422	chr1:246854862-247002638	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
8	nsv1011346	chr1:246868799-247133898	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
9	nsv1006262	chr1:246892826-246964775	Enhancers Weak transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
10	nsv523531	chr1:246893948-246967899	Enhancers Strong transcription Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
11	nsv999756	chr1:246894542-246969660	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
12	nsv1009436	chr1:246910373-246965832	Bivalent/Poised TSS Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
13	nsv873423	chr1:246923861-246978504	Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Weak transcription Active TSS Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs3314	LOC149134	cis	cerebellum	SCAN
rs3314	SCCPDH	cis	cerebellum	SCAN
rs3314	RGS7	cis	cerebellum	SCAN
rs3314	OR2T10	cis	parietal	SCAN

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:246888400-246946400	Weak transcription	Small Intestine	intestine
2	chr1:246888600-246945600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
3	chr1:246895000-246942200	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr1:246895400-246938600	Weak transcription	Fetal Heart	heart
5	chr1:246902800-246952800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr1:246904600-246942800	Weak transcription	Primary T cells fromperipheralblood	blood
7	chr1:246905000-246945800	Weak transcription	Psoas Muscle	Psoas
8	chr1:246905800-246931600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr1:246912600-246932200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr1:246912800-246933200	Weak transcription	K562	blood
11	chr1:246917600-246931200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr1:246917600-246936000	Weak transcription	Primary B cells from peripheral blood	blood
13	chr1:246920800-246931200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr1:246920800-246944200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr1:246921000-246931800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr1:246921200-246943200	Strong transcription	Dnd41	blood
17	chr1:246921600-246945800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
18	chr1:246922000-246932000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr1:246922000-246936400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr1:246922200-246931200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr1:246922200-246931200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr1:246922200-246932200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr1:246922200-246932800	Strong transcription	HepG2	liver
24	chr1:246922200-246933000	Strong transcription	Fetal Intestine Large	intestine
25	chr1:246922200-246934400	Strong transcription	Placenta	Placenta
26	chr1:246922200-246936000	Strong transcription	Primary neutrophils fromperipheralblood	blood
27	chr1:246922200-246936000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr1:246922200-246936200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr1:246922200-246937000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
30	chr1:246922200-246944600	Strong transcription	Fetal Muscle Trunk	muscle
31	chr1:246922400-246932200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr1:246922600-246936400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
33	chr1:246922800-246932000	Strong transcription	Osteobl	bone
34	chr1:246923000-246932200	Strong transcription	Adipose Nuclei	Adipose
35	chr1:246923000-246933000	Strong transcription	Primary T cells from cord blood	blood
36	chr1:246923000-246936200	Strong transcription	Primary hematopoietic stem cells	blood
37	chr1:246923200-246945000	Strong transcription	Fetal Muscle Leg	muscle
38	chr1:246923400-246932600	Strong transcription	Skeletal Muscle Male	skeletal muscle
39	chr1:246923600-246933200	Strong transcription	Brain Hippocampus Middle	brain
40	chr1:246924000-246941200	Strong transcription	Primary monocytes fromperipheralblood	blood
41	chr1:246924000-246944200	Strong transcription	Monocytes-CD14+_RO01746	blood
42	chr1:246924200-246931200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
43	chr1:246924400-246931400	Weak transcription	GM12878-XiMat	blood
44	chr1:246924400-246934600	Weak transcription	Fetal Brain Male	brain
45	chr1:246924400-246939200	Weak transcription	Colonic Mucosa	Colon
46	chr1:246924400-246945800	Weak transcription	Primary B cells from cord blood	blood
47	chr1:246924800-246931600	Weak transcription	H9 Cell Line	embryonic stem cell
48	chr1:246925200-246931600	Weak transcription	HUES48 Cell Line	embryonic stem cell
49	chr1:246925200-246952200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
50	chr1:246925400-246931600	Weak transcription	Spleen	Spleen

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