Variant report

Variant	rs10865143
Chromosome Location	chr2:38991956-38991957
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:38974221..38979921-chr2:38986851..38994572,21	K562	blood:
2	chr2:38973025..38976072-chr2:38989424..38992491,3	MCF-7	breast:
3	chr2:38991194..38992863-chr2:38993787..38996027,2	MCF-7	breast:
4	chr2:38976319..38979796-chr2:38988969..38996616,16	MCF-7	breast:
5	chr2:38973912..38980240-chr2:38989822..38999883,17	MCF-7	breast:
6	chr2:38991817..38994202-chr2:39346658..39349506,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000115875	Chromatin interaction
ENSG00000115904	Chromatin interaction
ENSG00000152147	Chromatin interaction

Extended variants
information (count: 93 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:89)

rs_ID	r²[population]
rs1010859	0.88[JPT][hapmap]
rs10173118	0.87[ASW][hapmap];0.92[CEU][hapmap];0.90[LWK][hapmap];0.95[MEX][hapmap];0.94[TSI][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10173240	0.88[CEU][hapmap];0.82[EUR][1000 genomes]
rs10197412	1.00[ASW][hapmap];0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[LWK][hapmap];0.96[MEX][hapmap];0.91[MKK][hapmap];0.89[TSI][hapmap];0.88[YRI][hapmap];0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10865144	0.82[EUR][1000 genomes]
rs1138975	0.85[ASN][1000 genomes]
rs11694383	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11898812	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12465043	0.81[EUR][1000 genomes]
rs12469681	0.89[EUR][1000 genomes]
rs12472454	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12473036	0.89[EUR][1000 genomes]
rs12474770	0.84[ASN][1000 genomes]
rs12477252	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12618118	1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12621103	0.90[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.83[ASN][1000 genomes]
rs12623330	0.81[CEU][hapmap]
rs12991609	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12996194	0.83[EUR][1000 genomes]
rs13011522	0.88[EUR][1000 genomes]
rs13014136	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13024811	0.91[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];0.83[ASN][1000 genomes]
rs13029406	0.86[ASW][hapmap];0.88[CEU][hapmap];0.83[LWK][hapmap];0.86[TSI][hapmap];0.84[EUR][1000 genomes]
rs13383541	0.88[CEU][hapmap];0.83[EUR][1000 genomes]
rs13411868	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13417196	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1529625	0.88[CEU][hapmap];0.91[CHB][hapmap];0.92[MEX][hapmap];0.86[TSI][hapmap];0.81[ASN][1000 genomes]
rs1530852	0.93[ASW][hapmap];0.96[CEU][hapmap];0.93[LWK][hapmap];0.96[MEX][hapmap];0.92[TSI][hapmap];0.88[EUR][1000 genomes]
rs1530853	0.93[ASW][hapmap];1.00[CEU][hapmap];0.88[LWK][hapmap];0.96[MEX][hapmap];0.92[TSI][hapmap];0.88[EUR][1000 genomes]
rs1979142	0.88[CEU][hapmap];0.82[EUR][1000 genomes]
rs1979143	0.90[CHB][hapmap];0.82[CHD][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs1997377	0.83[MEX][hapmap]
rs2037875	1.00[ASW][hapmap];0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[LWK][hapmap];0.96[MEX][hapmap];0.91[MKK][hapmap];0.92[TSI][hapmap];0.94[YRI][hapmap];0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2272445	0.83[TSI][hapmap]
rs3097713	0.91[CHB][hapmap];0.82[CHD][hapmap];0.87[GIH][hapmap];0.88[JPT][hapmap];0.80[ASN][1000 genomes]
rs3097714	0.88[CHD][hapmap];0.88[JPT][hapmap]
rs3099961	0.87[ASN][1000 genomes]
rs3099965	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3099968	0.90[CHB][hapmap];0.88[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs3099971	0.90[ASN][1000 genomes]
rs3099990	0.81[CHB][hapmap];1.00[JPT][hapmap]
rs3100000	1.00[JPT][hapmap]
rs3108666	0.80[ASN][1000 genomes]
rs3112140	0.82[EUR][1000 genomes]
rs3112142	0.81[CHB][hapmap]
rs3112152	0.80[ASN][1000 genomes]
rs3112156	0.80[ASN][1000 genomes]
rs3112159	0.88[JPT][hapmap]
rs3112161	0.80[ASN][1000 genomes]
rs3112163	1.00[JPT][hapmap]
rs3112178	0.90[CHB][hapmap];0.88[JPT][hapmap]
rs3112183	1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.86[ASN][1000 genomes]
rs3112184	1.00[CHB][hapmap];0.94[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs3112186	0.90[ASN][1000 genomes]
rs3112188	1.00[CHB][hapmap];0.88[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs3112189	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs3112191	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs3112192	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs3112194	0.86[ASN][1000 genomes]
rs3112196	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs3112198	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3112200	0.92[CEU][hapmap];0.83[MEX][hapmap];0.94[TSI][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3112204	0.87[ASN][1000 genomes]
rs3112205	0.88[EUR][1000 genomes]
rs3112210	0.88[EUR][1000 genomes]
rs3112216	0.80[EUR][1000 genomes]
rs3134628	0.83[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.86[ASN][1000 genomes]
rs3134629	0.86[ASN][1000 genomes]
rs3134630	0.86[ASN][1000 genomes]
rs3134637	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs35387882	0.90[ASN][1000 genomes]
rs3731838	0.91[CHB][hapmap];0.85[CHD][hapmap];0.84[GIH][hapmap];0.82[MEX][hapmap];0.81[TSI][hapmap];0.85[ASN][1000 genomes]
rs4602206	1.00[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4630748	1.00[CEU][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4670268	0.86[JPT][hapmap]
rs4670891	0.80[AFR][1000 genomes]
rs4670892	0.84[ASN][1000 genomes]
rs4670897	0.82[EUR][1000 genomes]
rs56393601	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs62144837	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6715866	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.97[TSI][hapmap];0.94[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6717670	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6728394	0.82[MEX][hapmap];0.84[TSI][hapmap]
rs6746818	1.00[CEU][hapmap];0.91[CHB][hapmap];0.89[ASN][1000 genomes]
rs6753251	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6756847	0.83[TSI][hapmap]
rs7419616	0.81[ASW][hapmap];1.00[CEU][hapmap];0.86[LWK][hapmap];0.91[MEX][hapmap];0.94[TSI][hapmap];0.88[EUR][1000 genomes]
rs7419838	0.92[CEU][hapmap];0.81[TSI][hapmap]
rs7589162	0.81[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916059	chr2:38332341-39119398	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	143 gene(s)	inside rSNPs	diseases
2	nsv9646	chr2:38358311-39082189	Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	141 gene(s)	inside rSNPs	diseases
3	esv1798055	chr2:38955865-39039504	Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	111 gene(s)	inside rSNPs	diseases
4	nsv1014616	chr2:38985472-39022893	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs10865143	DHX57	cis	multi-tissue	Pritchard
rs10865143	DHX57	cis	cerebellum	SCAN
rs10865143	MORN2	cis	parietal	SCAN
rs10865143	SFRS7	Cis_1M	lymphoblastoid	RTeQTL
rs10865143	DHX57	cis	parietal	SCAN

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:38979200-39005000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr2:38991200-38994200	Weak transcription	HepG2	liver
3	chr2:38991600-38992000	Enhancers	Pancreas	Pancrea
4	chr2:38991600-38992200	Enhancers	NHEK	skin
5	chr2:38991600-38992400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr2:38991600-38992600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr2:38991600-38993200	Enhancers	NH-A	brain
8	chr2:38991800-38993200	Enhancers	HMEC	breast
9	chr2:38991800-38993600	Enhancers	Osteobl	bone
10	chr2:38991800-38993800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr2:38991800-38994400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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