Variant report

Variant	rs3753516
Chromosome Location	chr1:209999135-209999136
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:209995353..209998573-chr1:209998823..210001196,6	K562	blood:
2	chr1:209977270..209980591-chr1:209996227..209999228,3	MCF-7	breast:
3	chr1:209998062..210000202-chr15:93873706..93875206,2	K562	blood:
4	chr1:209977871..209984485-chr1:209998424..210002427,6	K562	blood:
5	chr1:209984333..209986966-chr1:209996753..209999573,2	MCF-7	breast:
6	chr1:209991325..209994197-chr1:209997349..210000501,3	K562	blood:
7	chr1:209954974..209958320-chr1:209998061..209999630,3	MCF-7	breast:
8	chr1:209991113..209993100-chr1:209999001..210001316,2	K562	blood:
9	chr1:209977911..209983292-chr1:209996386..210001078,7	MCF-7	breast:
10	chr1:209997233..209999615-chr1:210545507..210547637,2	MCF-7	breast:
11	chr1:209839849..209842808-chr1:209998305..210001255,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000117595	Chromatin interaction
ENSG00000162757	Chromatin interaction
ENSG00000200972	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs11579771	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs583814	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs585191	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs593543	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs596731	0.83[EUR][1000 genomes]
rs597673	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs599021	0.94[ASN][1000 genomes]
rs599663	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs615276	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs623360	0.92[ASN][1000 genomes]
rs632305	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs648349	0.92[ASN][1000 genomes]
rs651141	0.94[ASN][1000 genomes]
rs661755	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs684083	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs846808	0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs861019	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999901	chr1:209600631-210205379	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
2	nsv1014034	chr1:209759648-210501731	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
3	nsv873139	chr1:209828955-210050794	Active TSS Enhancers Weak transcription Bivalent Enhancer Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3753516	SYT14	cis	Nerve Tibial	GTEx

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:209992600-210000800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr1:209996000-210000800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr1:209996600-209999200	Weak transcription	HSMMtube	muscle
4	chr1:209996600-210000400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
5	chr1:209996600-210000800	Weak transcription	Liver	Liver
6	chr1:209996600-210000800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
7	chr1:209996600-210000800	Enhancers	HMEC	breast
8	chr1:209996800-210000600	Weak transcription	Primary T helper cells PMA-I stimulated	--
9	chr1:209996800-210000800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
10	chr1:209996800-210000800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
11	chr1:209997000-209999200	Weak transcription	HepG2	liver
12	chr1:209997000-210000000	Weak transcription	Dnd41	blood
13	chr1:209997000-210000600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr1:209997000-210000600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr1:209997000-210000800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr1:209997000-210000800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
17	chr1:209997000-210000800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr1:209997000-210000800	Weak transcription	Brain Hippocampus Middle	brain
19	chr1:209997000-210000800	Weak transcription	Fetal Heart	heart
20	chr1:209997200-209999400	Weak transcription	A549	lung
21	chr1:209997200-210000800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr1:209997200-210000800	Weak transcription	HUES48 Cell Line	embryonic stem cell
23	chr1:209997200-210000800	Weak transcription	Pancreatic Islets	Pancreatic Islet
24	chr1:209997200-210000800	Weak transcription	Hela-S3	cervix
25	chr1:209997200-210000800	Weak transcription	HSMM	muscle
26	chr1:209997200-210001000	Weak transcription	Gastric	stomach
27	chr1:209997400-209999400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
28	chr1:209997400-209999600	Enhancers	HUVEC	blood vessel
29	chr1:209997400-210000600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr1:209997400-210000800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr1:209997400-210000800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr1:209997400-210000800	Weak transcription	Muscle Satellite Cultured Cells	--
33	chr1:209997400-210000800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr1:209997400-210000800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr1:209997400-210000800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr1:209997400-210000800	Weak transcription	Adipose Nuclei	Adipose
37	chr1:209997400-210000800	Weak transcription	Left Ventricle	heart
38	chr1:209997400-210000800	Weak transcription	NH-A	brain
39	chr1:209997400-210000800	Weak transcription	NHDF-Ad	bronchial
40	chr1:209997600-210000800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr1:209997600-210000800	Weak transcription	Osteobl	bone
42	chr1:209997800-209999800	Weak transcription	Rectal Mucosa Donor 31	rectum
43	chr1:209998200-210000600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
44	chr1:209998400-210000800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr1:209998600-209999200	Flanking Active TSS	NHEK	skin
46	chr1:209998600-210000600	Weak transcription	Primary T helper cells fromperipheralblood	blood
47	chr1:209998600-210000600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr1:209998800-209999400	Enhancers	K562	blood
49	chr1:209998800-209999600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
50	chr1:209998800-210000800	Enhancers	Fetal Intestine Large	intestine

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