Variant report

Variant	rs11966042
Chromosome Location	chr6:28368861-28368862
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:2 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	NFIC	chr6:28368858-28369375	SK-N-SH	brain:	n/a	n/a
2	FOS	chr6:28368850-28369297	MCF10A-Er-Src	breast:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:28315597..28319153-chr6:28366055..28369015,3	K562	blood:
2	chr6:28364231..28371937-chr6:28372195..28378158,17	K562	blood:
3	chr6:28367674..28369905-chr6:28510832..28512890,2	K562	blood:
4	chr6:28103668..28105670-chr6:28367426..28369293,3	K562	blood:
5	chr6:28044681..28046793-chr6:28367579..28369114,2	K562	blood:
6	chr6:28366328..28369247-chr6:28582607..28584582,2	K562	blood:
7	chr6:28368732..28370579-chr6:28448178..28450277,2	K562	blood:

No data

Variant related genes	Relation type
ZSCAN12	TF binding region
ENSG00000269293	Chromatin interaction
ENSG00000232040	Chromatin interaction
ENSG00000261839	Chromatin interaction
ENSG00000251877	Chromatin interaction
ENSG00000189298	Chromatin interaction

Extended variants
information (count: 67 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs1015810	0.91[EUR][1000 genomes]
rs1150669	0.91[EUR][1000 genomes]
rs1150671	0.91[EUR][1000 genomes]
rs11965542	1.00[EUR][1000 genomes]
rs11966237	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs11967622	0.82[ASW][hapmap];1.00[CEU][hapmap];0.85[TSI][hapmap];0.91[EUR][1000 genomes]
rs11969150	1.00[EUR][1000 genomes]
rs11970404	0.91[EUR][1000 genomes]
rs1233667	0.91[EUR][1000 genomes]
rs1233698	1.00[CEU][hapmap];0.85[TSI][hapmap];0.91[EUR][1000 genomes]
rs1233702	0.91[EUR][1000 genomes]
rs2078422	0.91[EUR][1000 genomes]
rs2108924	1.00[CEU][hapmap]
rs213227	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[YRI][hapmap];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs213235	1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2159274	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs2232439	1.00[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2531801	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[YRI][hapmap];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2531802	0.91[EUR][1000 genomes]
rs2531812	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs2531816	1.00[CEU][hapmap];1.00[CHD][hapmap];0.85[TSI][hapmap];0.82[EUR][1000 genomes]
rs2531819	0.91[EUR][1000 genomes]
rs2531826	1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2531828	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[YRI][hapmap];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28382592	0.82[EUR][1000 genomes]
rs2859349	0.91[EUR][1000 genomes]
rs2859350	0.91[EUR][1000 genomes]
rs2859353	0.82[EUR][1000 genomes]
rs2859354	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs2859359	1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2859362	1.00[EUR][1000 genomes]
rs2859367	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2859371	0.91[EUR][1000 genomes]
rs2859375	1.00[CEU][hapmap]
rs2859376	1.00[CEU][hapmap];1.00[CHD][hapmap];0.85[TSI][hapmap];0.91[EUR][1000 genomes]
rs2859377	0.91[EUR][1000 genomes]
rs2859378	0.91[EUR][1000 genomes]
rs2859379	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap]
rs385908	0.91[EUR][1000 genomes]
rs400987	0.91[EUR][1000 genomes]
rs403774	0.91[EUR][1000 genomes]
rs423118	0.91[EUR][1000 genomes]
rs59457415	1.00[EUR][1000 genomes]
rs61540948	0.91[EUR][1000 genomes]
rs62638680	1.00[EUR][1000 genomes]
rs6916243	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6932394	1.00[EUR][1000 genomes]
rs719370	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73385806	1.00[EUR][1000 genomes]
rs73385807	1.00[EUR][1000 genomes]
rs73385810	1.00[EUR][1000 genomes]
rs73385818	1.00[EUR][1000 genomes]
rs73385870	1.00[EUR][1000 genomes]
rs73387810	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73399084	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73400525	0.91[EUR][1000 genomes]
rs73400579	0.91[EUR][1000 genomes]
rs73400580	1.00[EUR][1000 genomes]
rs73400590	1.00[EUR][1000 genomes]
rs73401012	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73401666	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73402513	1.00[EUR][1000 genomes]
rs7739389	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7752608	1.00[ASN][1000 genomes]
rs7759845	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9468305	0.91[EUR][1000 genomes]
rs9468306	0.91[EUR][1000 genomes]

No data

Chromatin state (count:7 , 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	chr6:28368200-28369000	Enhancers	Muscle Satellite Cultured Cells	--
3	chr6:28368200-28369000	Enhancers	NHEK	skin
4	chr6:28368200-28369400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr6:28368400-28369600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr6:28368600-28371200	Enhancers	K562	blood
7	chr6:28368800-28369800	Weak transcription	GM12878-XiMat	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links