Variant report

Variant	rs28743126
Chromosome Location	chr12:124028131-124028132
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:124016543..124018893-chr12:124027101..124029081,2	K562	blood:
2	chr12:124014613..124020427-chr12:124021757..124030921,10	MCF-7	breast:
3	chr12:123982775..123984633-chr12:124027531..124030099,2	MCF-7	breast:
4	chr12:124016543..124019895-chr12:124027581..124031023,4	K562	blood:

Variant related genes	Relation type
ENSG00000188026	Chromatin interaction

Extended variants
information (count: 91 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:85)

rs_ID	r²[population]
rs1060638	1.00[ASN][1000 genomes]
rs11572911	0.92[EUR][1000 genomes]
rs11572914	1.00[ASN][1000 genomes]
rs11572916	1.00[ASN][1000 genomes]
rs11572919	1.00[ASN][1000 genomes]
rs11572921	1.00[ASN][1000 genomes]
rs11572928	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11572929	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11572931	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11572938	1.00[EUR][1000 genomes]
rs11572956	1.00[EUR][1000 genomes]
rs11572961	1.00[ASN][1000 genomes]
rs11572962	1.00[EUR][1000 genomes]
rs11572965	1.00[ASN][1000 genomes]
rs11572970	1.00[ASN][1000 genomes]
rs11572992	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11573002	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11573003	1.00[ASN][1000 genomes]
rs11573005	1.00[CEU][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11573006	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs11831129	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12099985	0.92[EUR][1000 genomes]
rs1568031	1.00[CEU][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17881657	1.00[EUR][1000 genomes]
rs1913847	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28627432	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28668364	0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs28711796	0.84[EUR][1000 genomes]
rs35917561	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3850953	0.92[EUR][1000 genomes]
rs4534668	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4930715	1.00[ASN][1000 genomes]
rs56816130	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57071951	1.00[ASN][1000 genomes]
rs58507743	1.00[ASN][1000 genomes]
rs58680194	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58831452	1.00[ASN][1000 genomes]
rs58904890	1.00[ASN][1000 genomes]
rs59279556	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59827616	1.00[ASN][1000 genomes]
rs60422010	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60577371	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61082817	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6488882	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs6488885	1.00[CEU][hapmap];0.82[GIH][hapmap];0.83[TSI][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6488886	0.92[EUR][1000 genomes]
rs6488889	1.00[CEU][hapmap];0.82[GIH][hapmap];0.83[TSI][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7134190	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7301031	0.92[EUR][1000 genomes]
rs7306906	0.92[EUR][1000 genomes]
rs7316613	1.00[ASN][1000 genomes]
rs73414295	1.00[ASN][1000 genomes]
rs73416203	1.00[ASN][1000 genomes]
rs73416204	1.00[ASN][1000 genomes]
rs73416211	1.00[ASN][1000 genomes]
rs73416216	1.00[ASN][1000 genomes]
rs73416265	1.00[EUR][1000 genomes]
rs73416269	1.00[EUR][1000 genomes]
rs73416277	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73416283	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73416288	1.00[ASN][1000 genomes]
rs73416298	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73416299	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73416301	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73418103	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73418104	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73418107	1.00[EUR][1000 genomes]
rs73418114	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73418125	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73418139	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73418148	1.00[ASN][1000 genomes]
rs73418153	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73418159	1.00[ASN][1000 genomes]
rs73418167	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73418174	1.00[ASN][1000 genomes]
rs73418179	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73418191	1.00[ASN][1000 genomes]
rs73420303	1.00[ASN][1000 genomes]
rs7964934	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs7965292	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs7965466	1.00[ASN][1000 genomes]
rs7968699	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7973187	0.92[EUR][1000 genomes]
rs7973689	1.00[CEU][hapmap];0.82[GIH][hapmap];0.83[TSI][hapmap];0.92[EUR][1000 genomes]
rs7974138	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.84[YRI][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1038841	chr12:123757305-124087671	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	nsv541622	chr12:123757305-124087671	Enhancers Strong transcription Genic enhancers Active TSS Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
3	nsv1050598	chr12:123991646-124214332	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
4	nsv541623	chr12:123991646-124214332	Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
5	nsv498024	chr12:123994372-124459856	Active TSS Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
6	esv2422416	chr12:124009676-124085689	Strong transcription Weak transcription Genic enhancers Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs28743126	GTF2H3	cis	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:124019400-124028200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin

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