Variant report

Variant	rs10161550
Chromosome Location	chr7:90706288-90706289
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	7:89975562-89981754..7:90704597-90714711	H1-hESC	embryonic stem cell:	embryo
2	7:90337078-90341001..7:90704597-90714711	GM12878	blood:
3	7:90224881-90229046..7:90704597-90714711	GM12878	blood:
4	7:90022908-90033390..7:90704597-90714711	GM12878	blood:
5	7:90185489-90196553..7:90704597-90714711	H1-hESC	embryonic stem cell:	embryo
6	7:89928454-89933690..7:90704597-90714711	H1-hESC	embryonic stem cell:	embryo
7	7:90090267-90099529..7:90704597-90714711	GM12878	blood:

Variant related genes	Relation type
ENSG00000273299	Chromatin interaction
ENSG00000251154	Chromatin interaction
ENSG00000157224	Chromatin interaction
ENSG00000223969	Chromatin interaction
ENSG00000105793	Chromatin interaction
ENSG00000105792	Chromatin interaction
ENSG00000058091	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10774152	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10774153	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10848715	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10848716	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10848814	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10848815	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11062302	0.89[AMR][1000 genomes]
rs11062385	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11611810	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1207323	0.81[AMR][1000 genomes]
rs12581260	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16929744	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16929783	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2052279	0.83[AMR][1000 genomes]
rs2229351	0.89[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2284332	0.88[AMR][1000 genomes]
rs2284333	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2284334	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2300131	0.86[ASN][1000 genomes]
rs3213750	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3753156	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3753157	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs479803	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs479836	0.82[AMR][1000 genomes]
rs479840	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs482514	0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs486098	0.84[EUR][1000 genomes]
rs4980811	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4980874	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4980877	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4980881	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4980885	0.83[AMR][1000 genomes]
rs4980886	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs576159	0.84[AMR][1000 genomes]
rs576994	0.84[AMR][1000 genomes]
rs61907027	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7132763	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7132845	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7134353	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7138981	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs720128	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7298995	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7301422	0.84[AMR][1000 genomes]
rs7303180	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7305580	0.80[EUR][1000 genomes]
rs7315852	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs764614	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7963309	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7963793	0.84[EUR][1000 genomes]
rs797759	0.81[AMR][1000 genomes]
rs887311	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[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	nsv532172	chr7:89950062-90792406	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10161550	JARID1A	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:90665800-90717400	Weak transcription	Lung	lung
2	chr7:90671200-90712800	Weak transcription	Fetal Muscle Leg	muscle
3	chr7:90671200-90741800	Weak transcription	Liver	Liver
4	chr7:90673000-90711600	Weak transcription	Cortex derived primary cultured neurospheres	brain
5	chr7:90675000-90713000	Weak transcription	Aorta	Aorta
6	chr7:90680600-90711400	Weak transcription	GM12878-XiMat	blood
7	chr7:90682800-90712600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr7:90685600-90713600	Weak transcription	Primary B cells from cord blood	blood
9	chr7:90694200-90711600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr7:90694600-90709400	Weak transcription	NHLF	lung
11	chr7:90694800-90708200	Weak transcription	Osteobl	bone
12	chr7:90694800-90708400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr7:90694800-90708400	Weak transcription	Muscle Satellite Cultured Cells	--
14	chr7:90696200-90707600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr7:90696400-90710400	Weak transcription	Rectal Smooth Muscle	rectum
16	chr7:90697000-90713600	Weak transcription	Fetal Stomach	stomach
17	chr7:90698800-90722400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr7:90701000-90719000	Weak transcription	Fetal Intestine Small	intestine
19	chr7:90701200-90725600	Weak transcription	Pancreas	Pancrea
20	chr7:90701400-90708400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
21	chr7:90701400-90726000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr7:90702000-90707600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr7:90702000-90708400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr7:90702000-90719000	Weak transcription	Fetal Muscle Trunk	muscle
25	chr7:90702200-90711400	Weak transcription	Primary B cells from peripheral blood	blood
26	chr7:90702200-90734400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links