Variant report

Variant	rs11204819
Chromosome Location	chr1:151435941-151435942
allele	C/T
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	MAFK	chr1:151435703-151435950	HepG2	liver:	n/a	chr1:151435801-151435821

No.	Distal block	Cell Line	Cell type
1	1:151411623-151426875..1:151434310-151436817	Hela-S3	cervix:
2	chr1:151429172..151433890-chr1:151435781..151441025,8	MCF-7	breast:
3	chr1:151427202..151436068-chr1:151477865..151490153,60	MCF-7	breast:
4	1:151434310-151436817..1:151618750-151636526	K562	blood:
5	chr1:151431741..151434239-chr1:151435568..151437628,2	K562	blood:
6	1:151434310-151436817..1:151516085-151535167	Hela-S3	cervix:

Variant related genes	Relation type
POGZ	TF binding region
ENSG00000207606	Chromatin interaction
ENSG00000143376	Chromatin interaction
ENSG00000223861	Chromatin interaction
ENSG00000143375	Chromatin interaction
ENSG00000143367	Chromatin interaction
ENSG00000143442	Chromatin interaction

Extended variants
information (count: 66 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs10736380	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10749662	0.86[EUR][1000 genomes]
rs11204807	0.92[CEU][hapmap];0.86[EUR][1000 genomes]
rs11204808	0.86[EUR][1000 genomes]
rs11204809	0.85[EUR][1000 genomes]
rs11204811	0.92[CEU][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes]
rs11204815	0.87[EUR][1000 genomes]
rs11204824	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.86[GIH][hapmap];0.90[JPT][hapmap];0.91[MEX][hapmap];0.96[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11578888	0.92[CEU][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes]
rs11583968	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11584694	0.86[EUR][1000 genomes]
rs11589645	0.85[EUR][1000 genomes]
rs11801791	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs12025432	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12029691	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12047617	0.86[EUR][1000 genomes]
rs12068166	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12068368	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12071705	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12120726	0.92[CEU][hapmap];0.88[EUR][1000 genomes]
rs12125310	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12740875	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12743850	0.84[CEU][hapmap]
rs12751531	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16833237	0.80[CHB][hapmap];0.94[JPT][hapmap];0.86[ASN][1000 genomes]
rs1887544	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1887545	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2274533	0.92[CEU][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes]
rs2274534	0.92[CEU][hapmap];1.00[TSI][hapmap];0.85[EUR][1000 genomes]
rs2274535	0.92[CEU][hapmap];0.86[EUR][1000 genomes]
rs2479379	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2479385	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2495380	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2864122	0.86[EUR][1000 genomes]
rs3118720	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34884031	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3748550	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3811409	0.89[JPT][hapmap]
rs3976737	0.92[CEU][hapmap];0.84[EUR][1000 genomes]
rs4246526	0.88[EUR][1000 genomes]
rs4246527	1.00[CEU][hapmap];0.86[CHB][hapmap];0.91[CHD][hapmap];0.96[GIH][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes]
rs4291502	1.00[ASW][hapmap];0.84[CEU][hapmap];1.00[MKK][hapmap]
rs4364884	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4528122	0.92[CEU][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes]
rs4603	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4971042	0.92[CEU][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes]
rs4971043	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4971047	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4971049	0.89[EUR][1000 genomes]
rs61818037	0.83[EUR][1000 genomes]
rs61818039	0.86[EUR][1000 genomes]
rs6587572	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6587573	0.86[EUR][1000 genomes]
rs6587577	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6587584	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6587585	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6684085	0.80[CHD][hapmap];0.92[GIH][hapmap];0.83[TSI][hapmap]
rs6684333	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6689436	0.86[EUR][1000 genomes]
rs7172	0.92[CEU][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes]
rs7542776	0.90[EUR][1000 genomes]
rs7546151	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7546933	0.86[EUR][1000 genomes]
rs9659456	0.87[ASN][1000 genomes]

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	nsv916272	chr1:150961809-151557253	Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	219 gene(s)	inside rSNPs	diseases
2	nsv831581	chr1:151289151-151478605	Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs11204819	SELENBP1	cis	cerebellum	SCAN
rs11204819	S100A4	cis	cerebellum	SCAN
rs11204819	POGZ	cis	cerebellum	SCAN
rs11204819	SELENBP1	cis	Thyroid	GTEx
rs11204819	SPRR2B	cis	parietal	SCAN
rs11204819	MRPS21	cis	parietal	SCAN

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:151431000-151445000	Weak transcription	Spleen	Spleen
2	chr1:151432400-151437800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr1:151432600-151436400	Weak transcription	Stomach Smooth Muscle	stomach
4	chr1:151432600-151436800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr1:151432600-151445000	Weak transcription	Fetal Intestine Small	intestine
6	chr1:151432600-151445000	Weak transcription	Pancreas	Pancrea

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links