Variant report

Variant	rs2025807
Chromosome Location	chr1:183943516-183943517
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:183942743..183945485-chr1:184021444..184023635,2	K562	blood:
2	chr1:183943457..183945002-chr1:183948434..183950269,2	K562	blood:
3	chr1:183943394..183945355-chr1:183948434..183952348,4	K562	blood:

Variant related genes	Relation type
ENSG00000198860	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10752927	0.85[CHB][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs10797925	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10797926	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10797927	0.82[ASN][1000 genomes]
rs10797928	0.85[CHB][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs10797929	0.82[ASW][hapmap];1.00[CEU][hapmap];0.85[CHB][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10797930	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10797932	0.91[JPT][hapmap]
rs10911475	0.81[EUR][1000 genomes]
rs10911477	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10911480	0.85[CHB][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs10911481	0.85[CHB][hapmap];0.95[JPT][hapmap];0.93[MKK][hapmap];0.82[ASN][1000 genomes]
rs10911482	0.85[CHB][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs10911483	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10911484	1.00[CEU][hapmap];0.88[CHB][hapmap];0.95[JPT][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10911485	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10911486	1.00[CEU][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];0.94[MEX][hapmap];0.83[TSI][hapmap];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12021841	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12023778	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12027096	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12028482	0.82[ASN][1000 genomes]
rs12030903	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12030924	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12034897	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12034962	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12042354	0.85[CHB][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs12044468	1.00[CEU][hapmap];0.89[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12059407	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12060999	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12061041	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12064779	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12069197	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12085344	1.00[CEU][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1475402	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs16861859	1.00[CEU][hapmap];0.85[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1887282	1.00[CEU][hapmap];0.95[JPT][hapmap];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1887283	1.00[CEU][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.83[TSI][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1926866	0.82[ASN][1000 genomes]
rs1926867	0.80[ASN][1000 genomes]
rs1926868	1.00[ASW][hapmap];1.00[CEU][hapmap];0.85[CHB][hapmap];0.89[GIH][hapmap];0.86[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1998926	0.80[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2148672	0.85[CHB][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs2148678	0.83[ASN][1000 genomes]
rs2182623	0.85[CHB][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs2182624	0.85[CHB][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs3930248	0.85[CHB][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs6662690	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6698329	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6701930	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7410829	0.82[ASW][hapmap];1.00[CEU][hapmap];0.85[CHB][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs751410	1.00[CEU][hapmap];0.85[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832026	chr1:183785065-183961847	Weak transcription Enhancers Genic enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv530079	chr1:183797938-184639971	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
3	nsv533206	chr1:183861204-184091272	Enhancers Weak transcription Active TSS Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
4	nsv1006655	chr1:183922288-184186677	Active TSS Flanking Active TSS Enhancers Bivalent Enhancer Strong transcription Weak transcription Flanking Bivalent TSS/Enh 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	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:183902600-183965200	Weak transcription	Left Ventricle	heart
2	chr1:183913000-183944800	Weak transcription	Fetal Stomach	stomach
3	chr1:183920200-183952600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr1:183923200-183961000	Weak transcription	Pancreas	Pancrea
5	chr1:183926600-183952200	Weak transcription	NHLF	lung
6	chr1:183938000-183946000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr1:183938000-183952200	Weak transcription	Skeletal Muscle Female	skeletal muscle
8	chr1:183938400-183952200	Weak transcription	Fetal Muscle Leg	muscle
9	chr1:183938600-183945400	Weak transcription	Stomach Smooth Muscle	stomach
10	chr1:183938600-183952800	Weak transcription	Fetal Muscle Trunk	muscle
11	chr1:183938800-183945600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr1:183938800-183946000	Strong transcription	Cortex derived primary cultured neurospheres	brain
13	chr1:183940200-183947600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr1:183940800-183944600	Weak transcription	Colon Smooth Muscle	Colon
15	chr1:183941000-183947400	Weak transcription	Brain Angular Gyrus	brain
16	chr1:183941400-183951200	Weak transcription	Brain Anterior Caudate	brain
17	chr1:183942000-183943600	Strong transcription	Brain Hippocampus Middle	brain
18	chr1:183942200-183945000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr1:183942200-183945000	Strong transcription	K562	blood
20	chr1:183942600-183944200	Strong transcription	Brain Cingulate Gyrus	brain
21	chr1:183942600-183945400	Strong transcription	Brain Inferior Temporal Lobe	brain
22	chr1:183943400-183946200	Weak transcription	Brain Substantia Nigra	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links