Variant report

Variant	rs8104751
Chromosome Location	chr19:39528203-39528204
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	CTCF	chr19:39528137-39529307	A549	lung:	n/a	chr19:39528990-39529008

No.	Distal block	Cell Line	Cell type
1	chr19:39526693..39529184-chr19:39566725..39569356,2	K562	blood:
2	chr19:39451089..39454157-chr19:39527302..39529882,3	MCF-7	breast:
3	chr19:39527434..39530385-chr19:39532161..39533802,2	K562	blood:
4	chr19:39519377..39524107-chr19:39526689..39529929,4	MCF-7	breast:
5	chr19:39520644..39523609-chr19:39524329..39528239,4	K562	blood:

Variant related genes	Relation type
FBXO27	TF binding region
ENSG00000267992	Chromatin interaction
ENSG00000161243	Chromatin interaction

Extended variants
information (count: 90 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:89)

rs_ID	r²[population]
rs10406222	0.90[ASN][1000 genomes]
rs10416823	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10417436	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10418645	0.81[AMR][1000 genomes]
rs10418648	0.82[AMR][1000 genomes]
rs10420169	0.82[AMR][1000 genomes]
rs10424632	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10424827	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10426645	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10426661	0.88[ASN][1000 genomes]
rs1062261	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10853723	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10853724	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11083499	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11083500	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11083501	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11083502	0.89[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.95[LWK][hapmap];0.91[MEX][hapmap];0.89[MKK][hapmap];0.95[TSI][hapmap];0.92[YRI][hapmap];0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1139251	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11667641	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11670486	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11670520	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11673044	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11673637	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11880441	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11883422	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12609806	1.00[CEU][hapmap];0.91[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.95[TSI][hapmap];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12610200	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12610248	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12971842	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12972850	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12972978	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12978163	0.90[ASN][1000 genomes]
rs12978749	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12982199	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12982349	0.92[ASN][1000 genomes]
rs12982529	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12985447	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1651748	0.86[EUR][1000 genomes]
rs1840745	0.94[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];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1840746	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1840747	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1840748	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1864191	0.80[AFR][1000 genomes];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1869983	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs36154890	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3848623	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4280369	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4802007	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4802009	0.87[ASN][1000 genomes]
rs4803181	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4803185	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4803186	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4803187	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4803188	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4803193	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs58897626	0.89[ASN][1000 genomes]
rs60775146	0.89[ASN][1000 genomes]
rs62119538	0.90[ASN][1000 genomes]
rs628335	0.87[ASN][1000 genomes]
rs650027	0.81[CEU][hapmap]
rs6508835	0.89[ASN][1000 genomes]
rs6508836	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6508837	0.89[ASN][1000 genomes]
rs6508838	0.92[ASN][1000 genomes]
rs6508839	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6508840	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6508841	0.95[CHB][hapmap];0.93[CHD][hapmap];0.87[JPT][hapmap];0.81[TSI][hapmap];0.92[ASN][1000 genomes]
rs6508842	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6508843	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs681496	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7247801	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7248513	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7248652	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7250110	0.83[AFR][1000 genomes];0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7250431	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7251264	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7255211	0.93[ASN][1000 genomes]
rs7256126	0.91[ASN][1000 genomes]
rs7258862	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7259064	0.88[ASN][1000 genomes]
rs7259197	1.00[CHB][hapmap];0.88[CHD][hapmap];0.84[GIH][hapmap];0.88[ASN][1000 genomes]
rs7259473	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7259801	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8100503	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8103187	0.88[ASN][1000 genomes]
rs8104899	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8104990	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8105865	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8109176	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[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	nsv963126	chr19:39521120-39552490	Weak transcription Enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs8104751	PSG3	cis	cerebellum	SCAN
rs8104751	CTB-189B5.3	cis	Esophagus Mucosa	GTEx
rs8104751	ZFP112	cis	parietal	SCAN
rs8104751	CTB-189B5.3	cis	Skin Sun Exposed Lower leg	GTEx
rs8104751	PPM1N	cis	parietal	SCAN
rs8104751	C19orf61	cis	cerebellum	SCAN
rs8104751	SNRPD2	cis	parietal	SCAN
rs8104751	FBXO27	cis	Skin Sun Exposed Lower leg	GTEx
rs8104751	FBXO27	cis	Esophagus Mucosa	GTEx
rs8104751	ZNF155	cis	parietal	SCAN
rs8104751	ARHGEF1	cis	parietal	SCAN

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:39523400-39529000	Weak transcription	Esophagus	oesophagus
2	chr19:39523400-39535400	Weak transcription	Right Atrium	heart
3	chr19:39523800-39528400	Weak transcription	HUES6 Cell Line	embryonic stem cell
4	chr19:39523800-39528600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr19:39523800-39528600	Weak transcription	Brain Substantia Nigra	brain
6	chr19:39523800-39528800	Weak transcription	Brain Cingulate Gyrus	brain
7	chr19:39523800-39528800	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr19:39523800-39528800	Weak transcription	K562	blood
9	chr19:39524400-39528600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr19:39524600-39528600	Weak transcription	Liver	Liver
11	chr19:39524800-39528600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr19:39525000-39528400	Weak transcription	NHEK	skin
13	chr19:39525000-39528600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr19:39525200-39528600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
15	chr19:39526800-39531400	Enhancers	Fetal Intestine Large	intestine
16	chr19:39527400-39528600	Enhancers	HepG2	liver
17	chr19:39527400-39529000	Enhancers	A549	lung
18	chr19:39527800-39529200	Enhancers	Placenta	Placenta
19	chr19:39528200-39528600	Weak transcription	Fetal Intestine Small	intestine

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links