Variant report

Variant	rs1366042
Chromosome Location	chr3:141183944-141183945
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:141079528..141080322-chr3:141183757..141184563,2	MCF-7	breast:
2	chr3:141179908..141182127-chr3:141182376..141185079,2	K562	blood:
3	chr3:141022193..141022928-chr3:141183865..141184712,2	MCF-7	breast:
4	chr3:141183744..141185593-chr3:141204841..141207517,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000155903	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs11711375	1.00[ASW][hapmap];1.00[CEU][hapmap];0.82[LWK][hapmap];0.95[MEX][hapmap];0.84[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.85[EUR][1000 genomes]
rs11916906	0.81[EUR][1000 genomes]
rs11917587	0.85[CEU][hapmap]
rs13069717	0.91[EUR][1000 genomes]
rs1493209	0.96[CEU][hapmap];0.85[EUR][1000 genomes]
rs1582875	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1863867	0.81[CEU][hapmap];0.95[YRI][hapmap];0.96[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs2042864	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2312193	0.96[CEU][hapmap];0.81[GIH][hapmap];0.91[MEX][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs295320	0.96[CEU][hapmap];0.82[MEX][hapmap];0.95[TSI][hapmap];0.80[EUR][1000 genomes]
rs295323	1.00[ASW][hapmap];0.92[CEU][hapmap];0.95[MEX][hapmap];0.92[TSI][hapmap];0.90[YRI][hapmap]
rs35711802	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3806646	0.96[CEU][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3821710	0.96[CEU][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.81[EUR][1000 genomes]
rs3821712	0.96[CEU][hapmap];0.95[MEX][hapmap];0.92[TSI][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6440013	0.80[EUR][1000 genomes]
rs6763498	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6767158	1.00[ASW][hapmap];0.96[CEU][hapmap];0.81[LWK][hapmap];0.87[MEX][hapmap];0.84[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6773734	0.97[ASN][1000 genomes]
rs6776003	0.85[CEU][hapmap]
rs6785874	1.00[ASW][hapmap];0.96[CEU][hapmap];0.81[LWK][hapmap];0.95[MEX][hapmap];0.84[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6795168	0.96[CEU][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6800122	1.00[ASW][hapmap];0.96[CEU][hapmap];0.81[LWK][hapmap];0.95[MEX][hapmap];0.84[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs6808837	0.96[CEU][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.91[EUR][1000 genomes]
rs7612543	0.88[CHB][hapmap];0.82[CHD][hapmap];0.90[GIH][hapmap];0.90[JPT][hapmap];0.83[MEX][hapmap];0.82[TSI][hapmap];0.83[ASN][1000 genomes]
rs7632308	0.92[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.97[TSI][hapmap];0.95[YRI][hapmap];0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7643837	1.00[ASW][hapmap];0.96[CEU][hapmap];0.85[LWK][hapmap];0.95[MEX][hapmap];0.86[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9289630	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9289631	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9813177	1.00[ASW][hapmap];0.96[CEU][hapmap];0.83[CHB][hapmap];0.91[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9851256	0.87[CEU][hapmap];0.81[EUR][1000 genomes]
rs9878347	0.81[CEU][hapmap];0.90[YRI][hapmap];0.86[AFR][1000 genomes]
rs9879503	0.81[CEU][hapmap];0.90[YRI][hapmap];0.87[AFR][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	nsv829744	chr3:141016749-141189168	Genic enhancers Strong transcription Transcr. at gene 5' and 3' Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs1366042	GK5	cis	parietal	SCAN
rs1366042	ATP1B3	cis	cerebellum	SCAN
rs1366042	RASA2	cis	parietal	SCAN
rs1366042	ZBTB38	cis	cerebellum	SCAN
rs1366042	RASA2	Cis_1M	lymphoblastoid	RTeQTL
rs1366042	RASA2	cis	cerebellum	SCAN

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:141177000-141184000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
2	chr3:141177000-141189600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr3:141178000-141184200	Weak transcription	NHLF	lung
4	chr3:141178000-141188200	Weak transcription	NHDF-Ad	bronchial
5	chr3:141179600-141184000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr3:141179600-141184000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr3:141179600-141184000	Weak transcription	Osteobl	bone
8	chr3:141181400-141184400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr3:141183600-141184600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr3:141183600-141184600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr3:141183800-141184200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr3:141183800-141184400	Enhancers	Muscle Satellite Cultured Cells	--
13	chr3:141183800-141184400	Enhancers	NH-A	brain
14	chr3:141183800-141184600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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