Variant report

Variant	rs4670689
Chromosome Location	chr2:37554962-37554963
allele	A/G
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	chr2:37554202-37555177	SK-N-SH	brain:	n/a	chr2:37554961-37554970 chr2:37554275-37554292 chr2:37554279-37554300 chr2:37554286-37554297
2	GATA3	chr2:37554458-37554992	SH-SY5Y	brain:	n/a	chr2:37554961-37554970
3	EP300	chr2:37554661-37555047	SK-N-SH_RA	brain:	n/a	n/a
4	GATA3	chr2:37553360-37555034	SK-N-SH	brain:	n/a	chr2:37554961-37554970 chr2:37554275-37554292 chr2:37554279-37554300 chr2:37554286-37554297
5	GATA2	chr2:37554265-37554994	SH-SY5Y	brain:	n/a	chr2:37554961-37554970 chr2:37554275-37554292 chr2:37554279-37554300 chr2:37554286-37554297
6	TCF12	chr2:37554166-37554982	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:37545726..37548175-chr2:37554305..37557162,2	K562	blood:
2	chr2:37543073..37544935-chr2:37554432..37557348,2	K562	blood:
3	chr2:37549953..37551637-chr2:37554820..37556399,2	K562	blood:
4	chr2:37553880..37556117-chr2:37565295..37568146,2	K562	blood:

Variant related genes	Relation type
PRKD3	TF binding region
ENSG00000115825	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10177176	0.82[CHB][hapmap]
rs10190959	0.87[CHB][hapmap];0.85[ASN][1000 genomes]
rs1056021	0.82[CHB][hapmap];0.82[JPT][hapmap]
rs11124569	0.81[JPT][hapmap]
rs11124574	0.82[CHB][hapmap]
rs11124578	1.00[CHB][hapmap];0.86[JPT][hapmap];0.92[YRI][hapmap];0.94[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs1158218	0.87[CHB][hapmap];0.89[ASN][1000 genomes]
rs1158219	0.91[CHB][hapmap];0.89[ASN][1000 genomes]
rs11682607	0.80[ASN][1000 genomes]
rs11689794	0.89[ASN][1000 genomes]
rs12616151	0.86[ASN][1000 genomes]
rs12618410	0.91[CHB][hapmap]
rs12712532	0.91[ASN][1000 genomes]
rs13015451	0.90[ASN][1000 genomes]
rs13030789	0.82[ASN][1000 genomes]
rs13420463	0.83[ASN][1000 genomes]
rs1477055	1.00[CHB][hapmap];0.91[JPT][hapmap];0.89[YRI][hapmap]
rs17020490	0.94[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs1989172	1.00[CHB][hapmap];0.82[JPT][hapmap];0.90[ASN][1000 genomes]
rs2268987	1.00[CHB][hapmap];0.82[JPT][hapmap];0.89[YRI][hapmap];0.91[ASN][1000 genomes]
rs2300881	1.00[CHB][hapmap];0.82[JPT][hapmap];0.93[ASN][1000 genomes]
rs2300884	1.00[CHB][hapmap];0.91[JPT][hapmap];0.94[YRI][hapmap];0.94[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs2302653	0.87[EUR][1000 genomes]
rs2372993	0.82[ASN][1000 genomes]
rs2888434	0.86[JPT][hapmap]
rs3770757	0.94[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs3770759	0.82[CHB][hapmap]
rs3819892	0.88[YRI][hapmap]
rs4581878	0.83[ASN][1000 genomes]
rs4670194	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4670195	0.91[CHB][hapmap];0.87[JPT][hapmap];0.94[ASN][1000 genomes]
rs4670688	1.00[CHB][hapmap];0.90[JPT][hapmap];0.89[YRI][hapmap];0.82[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs4998429	0.91[JPT][hapmap]
rs56774710	0.96[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs57361399	0.90[ASN][1000 genomes]
rs6544066	0.95[CHB][hapmap];0.82[JPT][hapmap];0.92[ASN][1000 genomes]
rs6734118	0.86[JPT][hapmap]
rs67467920	0.94[ASN][1000 genomes]
rs71398224	0.82[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs72792829	0.81[ASN][1000 genomes]
rs74177070	0.83[ASN][1000 genomes]
rs7568510	0.88[ASN][1000 genomes]
rs7570547	0.89[ASN][1000 genomes]
rs7584565	0.89[ASN][1000 genomes]
rs9309004	0.82[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv430724	chr2:37546820-37628704	Weak transcription Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	n/a
2	nsv2685	chr2:37550096-37594923	Active TSS Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:37553000-37555200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
2	chr2:37553200-37555000	Weak transcription	Small Intestine	intestine
3	chr2:37553800-37562200	Weak transcription	Primary monocytes fromperipheralblood	blood
4	chr2:37554000-37557800	Weak transcription	Monocytes-CD14+_RO01746	blood
5	chr2:37554400-37555000	Enhancers	NHDF-Ad	bronchial
6	chr2:37554800-37555000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr2:37554800-37555000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr2:37554800-37555200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links