Variant report

Variant	rs588983
Chromosome Location	chr1:114659419-114659420
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:114659207..114660324-chr1:114825081..114825855,3	MCF-7	breast:
2	chr1:114657959..114660485-chr1:114662733..114665313,2	K562	blood:
3	chr1:114657028..114661761-chr1:114663955..114667421,5	MCF-7	breast:
4	chr1:114656303..114663278-chr1:114663805..114668148,7	MCF-7	breast:
5	chr1:114657401..114660243-chr1:114668370..114670843,2	MCF-7	breast:

Extended variants
information (count: 21 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs12095538	0.88[CEU][hapmap];0.82[JPT][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1872478	0.96[CEU][hapmap];0.90[CHB][hapmap];0.84[YRI][hapmap];0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2481087	0.94[ASN][1000 genomes]
rs2629811	1.00[CHB][hapmap];0.82[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs2774309	0.95[CHB][hapmap];0.81[YRI][hapmap];0.82[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs2774310	0.95[CHB][hapmap];0.81[JPT][hapmap];0.81[YRI][hapmap];0.82[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs2774311	0.86[CHB][hapmap];0.92[CHD][hapmap];0.85[ASN][1000 genomes]
rs479359	0.90[CHB][hapmap];0.95[CHD][hapmap];0.91[ASN][1000 genomes]
rs498302	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs552581	0.82[ASW][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.81[JPT][hapmap];0.89[LWK][hapmap];0.97[MKK][hapmap];0.88[YRI][hapmap];0.87[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs633255	0.89[ASN][1000 genomes]
rs659646	0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs661871	0.95[CHB][hapmap];0.81[JPT][hapmap];0.81[YRI][hapmap];0.95[ASN][1000 genomes]
rs676268	0.82[ASN][1000 genomes]
rs677674	0.82[EUR][1000 genomes]
rs964592	0.84[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs964593	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs964594	0.85[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	esv2752424	chr1:114189958-114712958	Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
2	esv1849780	chr1:114577463-114663164	Enhancers Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS	Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	esv2752948	chr1:114658958-114751958	Enhancers Bivalent/Poised TSS Bivalent Enhancer Strong transcription Weak transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs588983	SYCP1	cis	parietal	SCAN

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:114630400-114675800	Weak transcription	Pancreas	Pancrea
2	chr1:114632200-114661000	Weak transcription	Brain Germinal Matrix	brain
3	chr1:114648800-114661600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr1:114649400-114661000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr1:114650800-114666000	Weak transcription	Brain Hippocampus Middle	brain
6	chr1:114652000-114660600	Weak transcription	Fetal Lung	lung
7	chr1:114654800-114661600	Enhancers	Primary monocytes fromperipheralblood	blood
8	chr1:114655600-114660600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr1:114655800-114659800	Weak transcription	Fetal Muscle Leg	muscle
10	chr1:114655800-114660000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr1:114655800-114662200	Enhancers	ES-I3 Cell Line	embryonic stem cell
12	chr1:114655800-114683800	Weak transcription	Right Atrium	heart
13	chr1:114656600-114661200	Strong transcription	HUES48 Cell Line	embryonic stem cell
14	chr1:114656800-114660600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr1:114656800-114660800	Strong transcription	H9 Cell Line	embryonic stem cell
16	chr1:114657000-114659800	Strong transcription	H1 Cell Line	embryonic stem cell
17	chr1:114657200-114659800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr1:114657200-114660600	Weak transcription	Skeletal Muscle Female	skeletal muscle
19	chr1:114657200-114660800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr1:114657200-114661000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr1:114657200-114661600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr1:114657200-114661800	Enhancers	Primary hematopoietic stem cells short term culture	blood
23	chr1:114657400-114660600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
24	chr1:114657600-114665600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr1:114657600-114665800	Weak transcription	Brain Anterior Caudate	brain
26	chr1:114657800-114660000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
27	chr1:114657800-114661600	Enhancers	Monocytes-CD14+_RO01746	blood
28	chr1:114658200-114666200	Genic enhancers	ES-UCSF4 Cell Line	embryonic stem cell
29	chr1:114658600-114661600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr1:114658800-114660200	Strong transcription	Fetal Brain Female	brain
31	chr1:114658800-114660600	Weak transcription	Primary hematopoietic stem cells	blood
32	chr1:114658800-114661200	Genic enhancers	HUES6 Cell Line	embryonic stem cell
33	chr1:114659400-114660400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
34	chr1:114659400-114660400	Genic enhancers	HUES64 Cell Line	embryonic stem cell
35	chr1:114659400-114662200	Genic enhancers	iPS-20b Cell Line	embryonic stem cell

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