Variant report

Variant	rs959141
Chromosome Location	chr2:48505401-48505402
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:48475464..48477949-chr2:48504616..48506328,2	K562	blood:
2	chr2:48496645..48499568-chr2:48504807..48506955,2	K562	blood:

Extended variants
information (count: 28 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs1509562	0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17037255	0.96[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs17397205	0.94[ASN][1000 genomes]
rs28439229	0.87[YRI][hapmap]
rs57729372	0.82[ASN][1000 genomes]
rs62137000	0.84[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs62138796	0.93[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs62138798	0.92[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs62138804	0.87[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs62138805	0.87[ASN][1000 genomes]
rs62138815	0.84[ASN][1000 genomes]
rs62138816	0.84[ASN][1000 genomes]
rs62138817	0.82[ASN][1000 genomes]
rs6545025	0.94[ASN][1000 genomes]
rs6545026	1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs6545031	0.85[LWK][hapmap];0.87[YRI][hapmap]
rs6545033	0.87[YRI][hapmap]
rs6738828	0.93[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs72820413	0.82[ASN][1000 genomes]
rs72820414	0.82[ASN][1000 genomes]
rs72887650	0.82[AFR][1000 genomes]
rs7563625	0.85[LWK][hapmap];0.87[YRI][hapmap]
rs7583112	0.93[AFR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1009769	chr2:47972642-48509765	Active TSS Bivalent Enhancer Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv535680	chr2:47972642-48509765	Genic enhancers Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
3	nsv530831	chr2:48059709-48632317	Enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
4	nsv519831	chr2:48072855-48566031	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
5	nsv1003766	chr2:48102244-48559654	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs959141	SOCS5	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:48505200-48505600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
2	chr2:48505200-48511600	Weak transcription	H1 Cell Line	embryonic stem cell
3	chr2:48505400-48505600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr2:48505400-48505800	Weak transcription	HUES64 Cell Line	embryonic stem cell
5	chr2:48505400-48505800	Weak transcription	GM12878-XiMat	blood
6	chr2:48505400-48506200	Weak transcription	Liver	Liver
7	chr2:48505400-48507600	Weak transcription	Psoas Muscle	Psoas
8	chr2:48505400-48513600	Weak transcription	Monocytes-CD14+_RO01746	blood

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