Variant report

Variant	rs10417436
Chromosome Location	chr19:39528932-39528933
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:39528736..39531074-chr19:39534796..39537090,2	K562	blood:
2	chr19:39526693..39529184-chr19:39566725..39569356,2	K562	blood:
3	chr19:39451089..39454157-chr19:39527302..39529882,3	MCF-7	breast:
4	chr19:39527434..39530385-chr19:39532161..39533802,2	K562	blood:
5	chr19:39519377..39524107-chr19:39526689..39529929,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000161243	Chromatin interaction
ENSG00000267992	Chromatin interaction

Extended variants
information (count: 87 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:86)

rs_ID	r²[population]
rs10406222	0.90[ASN][1000 genomes]
rs10416823	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10424632	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10424827	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10426645	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10426661	0.88[ASN][1000 genomes]
rs1062261	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10853723	0.99[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10853724	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11083499	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11083500	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11083501	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11083502	0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1139251	0.83[AMR][1000 genomes];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];0.95[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11670486	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11670520	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11673044	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11673637	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11880441	0.91[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];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12609806	0.94[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.83[MEX][hapmap];0.95[TSI][hapmap];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12610200	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12610248	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12971842	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12972850	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12972978	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12978163	0.90[ASN][1000 genomes]
rs12978749	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12982199	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12982349	0.92[ASN][1000 genomes]
rs12982529	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12985447	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1651748	0.85[EUR][1000 genomes]
rs1840745	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];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1840746	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1840747	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1840748	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1864191	0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1869983	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs36154890	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3848623	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4280369	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4802007	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4802009	0.87[ASN][1000 genomes]
rs4803181	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4803185	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4803186	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4803187	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4803188	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4803193	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap];0.81[AFR][1000 genomes];0.98[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	0.99[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	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6508840	0.94[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];0.84[MEX][hapmap];0.81[TSI][hapmap];0.92[ASN][1000 genomes]
rs6508842	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6508843	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs681496	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7247801	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7248513	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7248652	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7250110	0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7250431	0.88[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap];0.81[AFR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7251264	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7255211	0.93[ASN][1000 genomes]
rs7256126	0.91[ASN][1000 genomes]
rs7258862	0.87[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	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7259801	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8100503	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8103187	0.88[ASN][1000 genomes]
rs8104751	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]
rs8104899	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8104990	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8105865	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8109176	0.85[AMR][1000 genomes];0.83[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:10)

SNP	Gene	Cis/trans	Tissue	Source
rs10417436	ZNF155	cis	parietal	SCAN
rs10417436	SNRPD2	cis	parietal	SCAN
rs10417436	PSG3	cis	cerebellum	SCAN
rs10417436	ZFP112	cis	parietal	SCAN
rs10417436	CTB-189B5.3	cis	Esophagus Mucosa	GTEx
rs10417436	FBXO27	cis	Skin Sun Exposed Lower leg	GTEx
rs10417436	CTB-189B5.3	cis	Skin Sun Exposed Lower leg	GTEx
rs10417436	PPM1N	cis	parietal	SCAN
rs10417436	FBXO27	cis	Esophagus Mucosa	GTEx
rs10417436	ARHGEF1	cis	parietal	SCAN

Chromatin state (count:32 , 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	chr19:39526800-39531400	Enhancers	Fetal Intestine Large	intestine
4	chr19:39527400-39529000	Enhancers	A549	lung
5	chr19:39527800-39529200	Enhancers	Placenta	Placenta
6	chr19:39528400-39529000	Enhancers	HUES6 Cell Line	embryonic stem cell
7	chr19:39528400-39529000	Enhancers	NHEK	skin
8	chr19:39528600-39529000	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr19:39528600-39529000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr19:39528600-39529000	Enhancers	Breast Myoepithelial Primary Cells	Breast
11	chr19:39528600-39529000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr19:39528600-39529000	Enhancers	Liver	Liver
13	chr19:39528600-39529000	Enhancers	Brain Anterior Caudate	brain
14	chr19:39528600-39529000	Enhancers	Brain Substantia Nigra	brain
15	chr19:39528600-39529000	Flanking Active TSS	HepG2	liver
16	chr19:39528600-39529200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr19:39528600-39529200	Bivalent Enhancer	Adipose Nuclei	Adipose
18	chr19:39528600-39529400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr19:39528600-39530800	Enhancers	Fetal Intestine Small	intestine
20	chr19:39528800-39529000	Enhancers	HUES64 Cell Line	embryonic stem cell
21	chr19:39528800-39529000	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr19:39528800-39529000	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
23	chr19:39528800-39529000	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
24	chr19:39528800-39529000	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr19:39528800-39529000	Enhancers	Brain Cingulate Gyrus	brain
26	chr19:39528800-39529000	Enhancers	Brain Hippocampus Middle	brain
27	chr19:39528800-39529000	Enhancers	Brain Inferior Temporal Lobe	brain
28	chr19:39528800-39529000	Flanking Active TSS	Duodenum Mucosa	Duodenum
29	chr19:39528800-39529000	Enhancers	K562	blood
30	chr19:39528800-39529000	Flanking Active TSS	Osteobl	bone
31	chr19:39528800-39529200	Active TSS	Fetal Kidney	kidney
32	chr19:39528800-39529200	Bivalent Enhancer	Fetal Muscle Trunk	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links