Variant report

Variant	rs583814
Chromosome Location	chr1:210020971-210020972
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:210013064..210016584-chr1:210019890..210022757,3	MCF-7	breast:
2	chr1:210020851..210023605-chr1:210545790..210548349,3	MCF-7	breast:
3	chr1:210020112..210021677-chr1:210023510..210025199,2	K562	blood:

Variant related genes	Relation type
ENSG00000200972	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs11579771	1.00[CEU][hapmap];0.87[JPT][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2049997	0.83[AMR][1000 genomes]
rs2236906	0.91[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap]
rs2357231	0.96[YRI][hapmap]
rs3753516	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4844497	0.83[AMR][1000 genomes]
rs585191	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs593543	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs597673	0.88[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs599021	0.93[ASN][1000 genomes]
rs599663	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs615276	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs623360	0.80[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs632305	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs648349	0.90[ASN][1000 genomes]
rs651141	0.87[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs661755	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs684083	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs846808	0.93[ASN][1000 genomes]
rs861019	0.87[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.93[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
rs583814	SYT14	cis	Nerve Tibial	GTEx

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:210001800-210025000	Weak transcription	Stomach Mucosa	stomach
2	chr1:210001800-210034000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr1:210002000-210023800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr1:210002400-210032000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr1:210003200-210027800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr1:210003200-210028600	Strong transcription	Primary T cells fromperipheralblood	blood
7	chr1:210003200-210029400	Strong transcription	Fetal Muscle Trunk	muscle
8	chr1:210003400-210028000	Strong transcription	Monocytes-CD14+_RO01746	blood
9	chr1:210003400-210028400	Strong transcription	Primary B cells from peripheral blood	blood
10	chr1:210003600-210028000	Strong transcription	HUES64 Cell Line	embryonic stem cell
11	chr1:210003800-210028000	Strong transcription	HUES48 Cell Line	embryonic stem cell
12	chr1:210003800-210028200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
13	chr1:210003800-210028400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr1:210004000-210021400	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
15	chr1:210004000-210027600	Strong transcription	K562	blood
16	chr1:210004000-210027800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr1:210004000-210028000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr1:210004000-210028000	Strong transcription	Fetal Thymus	thymus
19	chr1:210004000-210028200	Strong transcription	Duodenum Mucosa	Duodenum
20	chr1:210004000-210030800	Strong transcription	Primary B cells from cord blood	blood
21	chr1:210004200-210022000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
22	chr1:210004200-210027600	Strong transcription	Primary monocytes fromperipheralblood	blood
23	chr1:210004200-210027600	Strong transcription	Primary hematopoietic stem cells	blood
24	chr1:210004200-210027600	Strong transcription	Rectal Mucosa Donor 31	rectum
25	chr1:210004200-210027800	Strong transcription	HUES6 Cell Line	embryonic stem cell
26	chr1:210004200-210027800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
27	chr1:210004200-210028000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr1:210004200-210028400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
29	chr1:210004200-210028400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
30	chr1:210004200-210028800	Strong transcription	Adipose Nuclei	Adipose
31	chr1:210004200-210029600	Strong transcription	Fetal Muscle Leg	muscle
32	chr1:210004200-210030200	Strong transcription	Primary T cells from cord blood	blood
33	chr1:210004400-210029400	Strong transcription	Dnd41	blood
34	chr1:210004600-210028000	Strong transcription	Primary T helper cells fromperipheralblood	blood
35	chr1:210004600-210028000	Strong transcription	GM12878-XiMat	blood
36	chr1:210006200-210025400	Strong transcription	Brain Hippocampus Middle	brain
37	chr1:210013200-210028800	Strong transcription	Fetal Intestine Large	intestine
38	chr1:210013400-210028800	Strong transcription	Liver	Liver
39	chr1:210013800-210022200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
40	chr1:210013800-210028000	Strong transcription	Primary T helper cells PMA-I stimulated	--
41	chr1:210013800-210029400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
42	chr1:210014200-210021600	Strong transcription	A549	lung
43	chr1:210014400-210021200	Strong transcription	Skeletal Muscle Female	skeletal muscle
44	chr1:210014400-210022600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr1:210014400-210028800	Strong transcription	NHEK	skin
46	chr1:210014400-210029400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr1:210014600-210022000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr1:210014600-210027600	Strong transcription	HSMM	muscle
49	chr1:210014600-210028200	Strong transcription	Hela-S3	cervix
50	chr1:210014800-210022400	Strong transcription	HMEC	breast

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