Variant report

Variant	rs13196606
Chromosome Location	chr6:28370078-28370079
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:1 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RCOR1	chr6:28369986-28370306	K562	blood:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:28364231..28371937-chr6:28372195..28378158,17	K562	blood:
2	chr6:28174164..28176650-chr6:28369447..28371283,2	K562	blood:
3	chr6:28369764..28371489-chr6:28380154..28383821,4	K562	blood:
4	chr6:28302778..28306478-chr6:28369638..28373643,3	K562	blood:
5	chr6:28368732..28370579-chr6:28448178..28450277,2	K562	blood:

No data

Variant related genes	Relation type
ZSCAN12	TF binding region
ENSG00000235109	Chromatin interaction
ENSG00000251877	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 16 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs1005126	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11751928	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.87[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs11755387	0.91[CHB][hapmap]
rs13190937	0.88[ASW][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.81[LWK][hapmap];0.84[MEX][hapmap];0.80[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs13193272	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13199081	0.95[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.93[YRI][hapmap];0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13203055	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13209596	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13215804	0.88[ASW][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.87[LWK][hapmap];0.89[MEX][hapmap];0.83[YRI][hapmap];0.81[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs13217326	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1361385	0.88[ASW][hapmap];0.81[MEX][hapmap]
rs16894011	0.91[CHB][hapmap]
rs16894091	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs16894106	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs16894116	0.81[CEU][hapmap]
rs16901847	0.81[CEU][hapmap]
rs17856167	0.91[CHB][hapmap]
rs2041230	0.82[ASW][hapmap];0.81[MEX][hapmap]
rs2232427	0.91[CHB][hapmap];0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28505234	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs3734563	0.88[ASW][hapmap];0.81[MEX][hapmap]
rs3799499	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3799500	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs3800328	0.81[ASW][hapmap]
rs4357130	0.88[ASW][hapmap];0.81[MEX][hapmap]
rs57071502	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs58020991	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6902687	1.00[CHB][hapmap];0.82[JPT][hapmap];0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs6905380	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6907950	0.88[ASW][hapmap];0.81[MEX][hapmap]
rs6908137	0.88[ASW][hapmap];0.81[MEX][hapmap]
rs6931359	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6940744	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs71559081	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7740429	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7750526	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7754960	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7764722	0.88[ASW][hapmap];0.81[MEX][hapmap]
rs7774981	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9461458	0.88[ASW][hapmap];0.81[MEX][hapmap]
rs9468355	0.88[ASW][hapmap]
rs9468356	0.84[CHB][hapmap];0.93[JPT][hapmap];0.90[YRI][hapmap];0.88[AFR][1000 genomes];0.81[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs9468358	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.88[AFR][1000 genomes];0.81[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs9468364	0.90[CHB][hapmap];0.81[ASN][1000 genomes]
rs9468370	0.88[ASW][hapmap];0.81[MEX][hapmap]
rs9969098	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]

mRNA abundance (count:16)

SNP	Gene	Cis/trans	Tissue	Source
rs13196606	NKAPL	cis	parietal	SCAN
rs13196606	TRIM38	cis	cerebellum	SCAN
rs13196606	ZSCAN23	cis	Artery Tibial	GTEx
rs13196606	ZSCAN12	Cis_1M	lymphoblastoid	RTeQTL
rs13196606	BTN3A2	cis	multi-tissue	Pritchard
rs13196606	ZSCAN23	cis	cerebellum	SCAN
rs13196606	RP5-874C20.3	cis	Esophagus Muscularis	GTEx
rs13196606	HLA-H	cis	multi-tissue	Pritchard
rs13196606	ZNF192	cis	cerebellum	SCAN
rs13196606	HLA-A	cis	multi-tissue	Pritchard
rs13196606	ZSCAN23	cis	parietal	SCAN
rs13196606	BTN3A2///BTN3A3	Cis_chr	lymphoblastoid	RTeQTL
rs13196606	BTN3A2	Cis_chr	lymphoblastoid	RTeQTL
rs13196606	ZNF323	cis	parietal	SCAN
rs13196606	AL022393.7	cis	Muscle Skeletal	GTEx
rs13196606	ZNF187	cis	cerebellum	SCAN

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28368000-28370800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr6:28368600-28371200	Enhancers	K562	blood
3	chr6:28370000-28370200	Bivalent Enhancer	H1 Cell Line	embryonic stem cell

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