Variant report

Variant	rs40928
Chromosome Location	chr7:108191625-108191626
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:108166940..108169062-chr7:108189842..108192603,2	K562	blood:
2	chr7:108190740..108192459-chr7:108199194..108201083,2	MCF-7	breast:
3	chr7:108175205..108176864-chr7:108190945..108193646,2	K562	blood:
4	chr7:108191362..108206184-chr7:108206645..108216261,27	K562	blood:
5	chr7:108184554..108188738-chr7:108190088..108193231,5	K562	blood:

Variant related genes	Relation type
ENSG00000177683	Chromatin interaction
ENSG00000128590	Chromatin interaction
ENSG00000135241	Chromatin interaction

Extended variants
information (count: 62 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs10487859	0.90[CHD][hapmap];0.81[GIH][hapmap];0.89[JPT][hapmap];0.86[ASN][1000 genomes]
rs11974559	0.90[CHD][hapmap];0.81[GIH][hapmap];0.89[JPT][hapmap];0.90[ASN][1000 genomes]
rs11981670	0.89[JPT][hapmap];0.86[ASN][1000 genomes]
rs12666562	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13229488	0.89[JPT][hapmap];0.86[ASN][1000 genomes]
rs17155828	0.86[ASN][1000 genomes]
rs17424206	0.86[ASN][1000 genomes]
rs194587	0.86[ASN][1000 genomes]
rs3202837	0.86[ASN][1000 genomes]
rs34814097	0.86[ASN][1000 genomes]
rs34887057	0.86[ASN][1000 genomes]
rs35372181	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35880371	0.86[ASN][1000 genomes]
rs3763457	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs40843	0.90[CHD][hapmap];0.81[GIH][hapmap];0.89[JPT][hapmap];0.86[ASN][1000 genomes]
rs40845	0.90[CHD][hapmap];0.89[JPT][hapmap];0.86[ASN][1000 genomes]
rs40850	0.86[ASN][1000 genomes]
rs40854	0.86[ASN][1000 genomes]
rs40872	0.89[JPT][hapmap];0.90[ASN][1000 genomes]
rs40875	0.90[ASN][1000 genomes]
rs40878	0.89[JPT][hapmap];0.90[ASN][1000 genomes]
rs40880	0.90[ASN][1000 genomes]
rs40882	0.86[ASN][1000 genomes]
rs40885	0.90[CHD][hapmap];0.81[GIH][hapmap];0.89[JPT][hapmap];0.90[ASN][1000 genomes]
rs40886	0.88[JPT][hapmap];0.90[ASN][1000 genomes]
rs40895	0.90[ASN][1000 genomes]
rs40899	0.90[CHD][hapmap];0.81[GIH][hapmap];0.89[JPT][hapmap];0.90[ASN][1000 genomes]
rs40900	0.89[JPT][hapmap];0.90[ASN][1000 genomes]
rs40901	0.90[ASN][1000 genomes]
rs40902	0.90[CHD][hapmap];0.81[GIH][hapmap];0.89[JPT][hapmap];0.90[ASN][1000 genomes]
rs40908	0.89[JPT][hapmap];0.90[ASN][1000 genomes]
rs40910	0.89[JPT][hapmap];0.90[ASN][1000 genomes]
rs40912	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs40914	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs40915	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs40919	0.96[CEU][hapmap];0.95[GIH][hapmap];0.89[JPT][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs40921	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs40923	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs40924	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs40925	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]
rs40926	0.96[CEU][hapmap];0.82[CHB][hapmap];0.95[GIH][hapmap];0.89[JPT][hapmap];0.80[LWK][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs40931	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs40932	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs40934	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs40936	0.96[CEU][hapmap];0.82[CHB][hapmap];0.95[GIH][hapmap];0.89[JPT][hapmap];0.90[MEX][hapmap];0.91[TSI][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs40938	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs40939	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs40940	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs40941	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];0.97[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs40942	0.96[CEU][hapmap];0.82[CHB][hapmap];0.89[JPT][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs40944	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs40945	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs40946	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs40947	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs40948	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs60426977	0.86[ASN][1000 genomes]
rs6466238	0.90[CHD][hapmap];0.81[GIH][hapmap];0.89[JPT][hapmap];0.86[ASN][1000 genomes]
rs67694466	0.86[ASN][1000 genomes]
rs6947492	0.89[JPT][hapmap];0.86[ASN][1000 genomes]
rs6955152	0.86[ASN][1000 genomes]
rs71568528	0.90[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3348839	chr7:107377311-108286538	Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	91 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs40928	THAP5	cis	multi-tissue	Pritchard
rs40928	THAP5	cis	Muscle Skeletal	GTEx
rs40928	THAP5	cis	normal skin	skin_eQTL
rs40928	THAP5	cis	lymphoblastoid	seeQTL
rs40928	THAP5	cis	uninvolved skin	skin_eQTL
rs40928	THAP5	cis	Esophagus Muscularis	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:108189000-108196800	Weak transcription	Cortex derived primary cultured neurospheres	brain
2	chr7:108190200-108195400	Weak transcription	Left Ventricle	heart
3	chr7:108190200-108201400	Weak transcription	HSMMtube	muscle
4	chr7:108191000-108192400	Enhancers	Primary B cells from cord blood	blood
5	chr7:108191200-108192600	Enhancers	Primary B cells from peripheral blood	blood
6	chr7:108191400-108204600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr7:108191600-108196800	Weak transcription	Ovary	ovary

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links