Variant report

Variant	rs1954713
Chromosome Location	chr8:110630440-110630441
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr8:110619769..110620594-chr8:110630256..110631117,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000147642	Chromatin interaction

Extended variants
information (count: 78 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs10100734	0.86[EUR][1000 genomes]
rs12678956	1.00[LWK][hapmap];1.00[MKK][hapmap]
rs13253969	0.85[ASN][1000 genomes]
rs13254530	0.86[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs13254967	0.85[ASN][1000 genomes]
rs13270118	0.83[EUR][1000 genomes]
rs16879844	0.86[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs1892758	0.86[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs1954714	0.86[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs2022930	0.89[CEU][hapmap];0.86[CHB][hapmap];0.80[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.85[ASN][1000 genomes]
rs2154656	1.00[CEU][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2154658	0.89[CEU][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2236627	1.00[LWK][hapmap];0.82[MEX][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];0.85[EUR][1000 genomes]
rs2703379	0.86[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs2703380	0.84[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs2703381	0.85[ASN][1000 genomes]
rs2703383	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2703390	0.85[EUR][1000 genomes]
rs2703391	0.86[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs2844238	0.86[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs2844239	0.86[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs2844240	0.86[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs2844241	0.86[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs2844242	0.86[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs2844243	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2844244	0.86[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs2844245	0.86[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs2844246	0.86[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs2844247	0.86[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs2844248	0.85[ASN][1000 genomes]
rs2844249	0.86[ASN][1000 genomes]
rs2844250	0.89[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs3108830	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3108834	0.83[EUR][1000 genomes]
rs3108835	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3108836	0.83[EUR][1000 genomes]
rs3108841	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3108855	0.89[CEU][hapmap];0.82[EUR][1000 genomes]
rs3108867	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3133920	0.86[EUR][1000 genomes]
rs3133923	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3133931	0.83[EUR][1000 genomes]
rs3133932	0.83[EUR][1000 genomes]
rs3133933	0.89[CEU][hapmap];0.83[EUR][1000 genomes]
rs3133938	0.81[EUR][1000 genomes]
rs3133939	0.81[EUR][1000 genomes]
rs3134316	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3134318	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3134326	0.86[EUR][1000 genomes]
rs3134328	0.86[EUR][1000 genomes]
rs3134329	0.86[EUR][1000 genomes]
rs3134332	0.82[EUR][1000 genomes]
rs3134333	0.81[EUR][1000 genomes]
rs3134335	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3134336	0.81[EUR][1000 genomes]
rs3134337	0.89[CEU][hapmap];0.81[EUR][1000 genomes]
rs3134338	0.89[CEU][hapmap];0.81[GIH][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes]
rs3134342	0.82[EUR][1000 genomes]
rs34147744	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34649979	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35642643	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3808380	1.00[LWK][hapmap]
rs4367512	0.86[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs61152293	0.85[ASN][1000 genomes]
rs6469270	0.86[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs6469271	0.86[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs6469272	0.86[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs6469273	0.86[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs6469274	0.89[CEU][hapmap];0.80[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs6982034	0.86[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs6994349	0.85[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs7003380	0.86[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs7003744	0.84[ASN][1000 genomes]
rs71526740	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7813979	0.86[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs7825702	0.85[ASN][1000 genomes]
rs9656885	0.87[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	esv1849702	chr8:110594148-110683804	Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs1954713	PKHD1L1	Cis_1M	lymphoblastoid	RTeQTL
rs1954713	PKHD1L1	cis	lymphoblastoid	seeQTL
rs1954713	SYBU	cis	parietal	SCAN
rs1954713	EIF3E	cis	parietal	SCAN
rs1954713	PKHD1L1	cis	multi-tissue	Pritchard
rs1954713	SYBU	cis	cerebellum	SCAN
rs1954713	TRHR	cis	parietal	SCAN

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:110590200-110654800	Weak transcription	Lung	lung
2	chr8:110617400-110632800	Weak transcription	Gastric	stomach
3	chr8:110617800-110632800	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr8:110620400-110631000	Weak transcription	Pancreas	Pancrea
5	chr8:110620400-110632200	Weak transcription	HMEC	breast
6	chr8:110620400-110632800	Weak transcription	Brain Substantia Nigra	brain
7	chr8:110620400-110651200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr8:110620400-110654800	Weak transcription	Esophagus	oesophagus
9	chr8:110621200-110654800	Weak transcription	Fetal Brain Female	brain
10	chr8:110622200-110632000	Strong transcription	Liver	Liver
11	chr8:110622600-110635200	Weak transcription	Fetal Brain Male	brain
12	chr8:110623000-110637800	Weak transcription	Left Ventricle	heart
13	chr8:110623400-110635200	Weak transcription	Small Intestine	intestine
14	chr8:110623400-110655000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr8:110623600-110632800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr8:110624200-110634600	Weak transcription	Rectal Mucosa Donor 29	rectum
17	chr8:110625000-110633000	Weak transcription	Ovary	ovary
18	chr8:110626200-110654800	Weak transcription	Brain Anterior Caudate	brain
19	chr8:110626600-110632600	Weak transcription	Hela-S3	cervix
20	chr8:110626600-110633800	Weak transcription	HepG2	liver
21	chr8:110627000-110631400	Strong transcription	Stomach Smooth Muscle	stomach
22	chr8:110627000-110633800	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr8:110627200-110633800	Weak transcription	Skeletal Muscle Female	skeletal muscle
24	chr8:110627200-110638800	Weak transcription	Right Atrium	heart
25	chr8:110627400-110631000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr8:110627400-110631200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr8:110627600-110638800	Weak transcription	Brain Angular Gyrus	brain
28	chr8:110628000-110632800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
29	chr8:110628800-110631600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
30	chr8:110628800-110631600	Strong transcription	Duodenum Mucosa	Duodenum
31	chr8:110629000-110631000	Strong transcription	NHEK	skin
32	chr8:110629400-110631000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr8:110629400-110631400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr8:110629800-110651800	Weak transcription	Rectal Mucosa Donor 31	rectum
35	chr8:110630000-110630800	Strong transcription	Primary B cells from peripheral blood	blood
36	chr8:110630000-110632000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr8:110630200-110631400	Genic enhancers	Adipose Nuclei	Adipose

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links