Variant report

Variant	rs2196488
Chromosome Location	chr12:29299549-29299550
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 24 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10492385	0.92[ASW][hapmap];0.89[CEU][hapmap];0.91[CHB][hapmap];0.85[CHD][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap];0.97[LWK][hapmap];0.86[MEX][hapmap];0.84[MKK][hapmap];0.84[TSI][hapmap];0.88[YRI][hapmap];0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs10771493	0.85[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10843342	0.86[JPT][hapmap]
rs11050079	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11050088	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11050111	0.86[JPT][hapmap]
rs11050117	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11830434	0.85[LWK][hapmap];0.94[YRI][hapmap]
rs12371983	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs12821923	0.86[JPT][hapmap]
rs16934002	0.86[JPT][hapmap]
rs4414260	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4931157	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4931166	0.92[ASW][hapmap];0.89[CEU][hapmap];0.87[GIH][hapmap];1.00[LWK][hapmap];0.82[MEX][hapmap];0.84[MKK][hapmap];0.84[TSI][hapmap];0.88[YRI][hapmap];0.80[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs6487782	0.88[YRI][hapmap];0.85[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs7296314	0.89[CEU][hapmap];0.91[CHB][hapmap];0.81[JPT][hapmap];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7302742	0.85[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap]
rs7968726	0.82[JPT][hapmap]
rs7969731	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[EUR][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	nsv532233	chr12:29009388-29496179	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv995123	chr12:29095272-29571558	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
3	nsv1053641	chr12:29268813-29854413	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
4	nsv819469	chr12:29285461-29303486	Flanking Active TSS Bivalent/Poised TSS Enhancers Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	esv3337951	chr12:29288734-29303032	Active TSS Enhancers Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2196488	SSPN	cis	parietal	SCAN
rs2196488	RP11-996F15.2	cis	lung	GTEx

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:29298400-29299600	Enhancers	H1 Cell Line	embryonic stem cell
2	chr12:29298400-29299600	Enhancers	HUES6 Cell Line	embryonic stem cell
3	chr12:29298600-29300600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr12:29298600-29301000	Weak transcription	Fetal Muscle Trunk	muscle
5	chr12:29298800-29299600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr12:29298800-29300000	Enhancers	Primary hematopoietic stem cells	blood
7	chr12:29299000-29299600	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr12:29299000-29300600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr12:29299000-29301200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr12:29299200-29299800	Enhancers	Primary hematopoietic stem cells short term culture	blood
11	chr12:29299200-29300800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
12	chr12:29299400-29300400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr12:29299400-29300600	Weak transcription	iPS-18 Cell Line	embryonic stem cell

Quick Search:

Input of quick search could be:

dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

what's new

Quick links