Variant report

Variant	rs1905538
Chromosome Location	chr10:118760270-118760271
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:118754411..118757627-chr10:118759486..118762210,3	MCF-7	breast:
2	chr10:118756628..118761775-chr10:118762306..118766688,9	MCF-7	breast:
3	chr10:118750321..118751905-chr10:118758831..118760527,2	K562	blood:

Variant related genes	Relation type
ENSG00000187164	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10218905	1.00[CEU][hapmap];0.87[CHB][hapmap];0.91[CHD][hapmap];0.81[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10510025	1.00[CEU][hapmap];0.86[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap];0.82[EUR][1000 genomes]
rs10787735	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10886016	0.80[CEU][hapmap];0.86[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap];0.84[EUR][1000 genomes]
rs10886017	0.83[EUR][1000 genomes]
rs10886021	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11197863	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1122688	1.00[CEU][hapmap];0.87[CHB][hapmap];0.93[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11593277	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11598817	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12769006	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1419832	1.00[ASW][hapmap];0.80[CEU][hapmap];0.86[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];0.91[MKK][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1637570	0.95[JPT][hapmap]
rs1637572	0.89[CHD][hapmap];0.81[GIH][hapmap];0.91[JPT][hapmap];0.86[MEX][hapmap]
rs1905542	0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1905544	0.93[ASW][hapmap];0.89[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.87[TSI][hapmap];0.88[YRI][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2101264	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.97[TSI][hapmap];0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2118207	0.93[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.87[YRI][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2170862	0.81[MEX][hapmap]
rs2257791	0.85[TSI][hapmap]
rs2531685	0.94[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs2531686	0.80[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs2531689	0.85[CHB][hapmap];0.94[JPT][hapmap];0.82[EUR][1000 genomes]
rs2627194	0.80[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs2627197	0.88[CHD][hapmap];0.91[JPT][hapmap];0.86[MEX][hapmap]
rs3781566	0.83[CEU][hapmap];0.83[JPT][hapmap]
rs4092881	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4638225	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6585422	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7074047	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7077565	0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7079724	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7083142	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7087685	0.86[MEX][hapmap]
rs7089699	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs719012	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs740600	1.00[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];0.90[MKK][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs7901788	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7903295	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs879255	0.83[CEU][hapmap];0.83[JPT][hapmap]
rs9420215	0.81[MEX][hapmap]

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	esv2755506	chr10:118748764-118800107	Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1905538	PNLIPRP2	cis	cerebellum	SCAN
rs1905538	KIAA1598	cis	Whole Blood	GTEx

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:118721600-118764000	Weak transcription	Ovary	ovary
2	chr10:118725200-118763000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr10:118735000-118762800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr10:118737200-118762800	Weak transcription	NHEK	skin
5	chr10:118738800-118762800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr10:118745000-118760400	Weak transcription	K562	blood
7	chr10:118747400-118763000	Weak transcription	HUVEC	blood vessel
8	chr10:118750200-118764000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr10:118751600-118763800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr10:118752400-118763600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr10:118752400-118764000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr10:118755000-118760400	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr10:118755600-118763800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr10:118755800-118760400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
15	chr10:118756600-118761400	Weak transcription	Liver	Liver
16	chr10:118756800-118761400	Weak transcription	A549	lung
17	chr10:118756800-118763200	Weak transcription	Rectal Mucosa Donor 29	rectum
18	chr10:118756800-118763600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr10:118757000-118761000	Weak transcription	HepG2	liver
20	chr10:118757200-118763600	Weak transcription	Rectal Mucosa Donor 31	rectum
21	chr10:118757400-118762800	Weak transcription	Fetal Intestine Large	intestine
22	chr10:118758400-118760400	Enhancers	Brain Hippocampus Middle	brain
23	chr10:118758600-118761400	Weak transcription	Hela-S3	cervix
24	chr10:118759000-118763600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr10:118759600-118760400	Enhancers	Brain Cingulate Gyrus	brain
26	chr10:118759600-118760800	Enhancers	Brain Anterior Caudate	brain
27	chr10:118759600-118760800	Enhancers	Brain Substantia Nigra	brain
28	chr10:118759600-118761600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr10:118760000-118760600	Active TSS	Brain Angular Gyrus	brain
30	chr10:118760000-118763600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
31	chr10:118760000-118763800	Enhancers	Primary monocytes fromperipheralblood	blood
32	chr10:118760200-118760400	Enhancers	Brain Inferior Temporal Lobe	brain
33	chr10:118760200-118760400	Enhancers	Fetal Brain Female	brain
34	chr10:118760200-118760400	Genic enhancers	Pancreas	Pancrea
35	chr10:118760200-118760600	Enhancers	HUES48 Cell Line	embryonic stem cell
36	chr10:118760200-118760800	Enhancers	iPS-15b Cell Line	embryonic stem cell
37	chr10:118760200-118761000	Flanking Active TSS	Brain Germinal Matrix	brain
38	chr10:118760200-118763600	Enhancers	Monocytes-CD14+_RO01746	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links