Variant report

Variant	rs3112184
Chromosome Location	chr2:38992584-38992585
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:10)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:10 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MYC	chr2:38992350-38992650	MCF10A-Er-Src	breast:	n/a	n/a
2	FOS	chr2:38992346-38992653	MCF10A-Er-Src	breast:	n/a	n/a
3	TCF12	chr2:38992087-38992688	SK-N-SH	brain:	n/a	n/a
4	FOS	chr2:38992346-38992616	MCF10A-Er-Src	breast:	n/a	n/a
5	GATA3	chr2:38992163-38992818	SK-N-SH	brain:	n/a	n/a
6	E2F4	chr2:38992344-38992614	MCF10A-Er-Src	breast:	n/a	n/a
7	FOS	chr2:38992350-38992613	MCF10A-Er-Src	breast:	n/a	n/a
8	NFIC	chr2:38992054-38992856	SK-N-SH	brain:	n/a	n/a
9	STAT3	chr2:38992333-38992584	MCF10A-Er-Src	breast:	n/a	n/a
10	FOS	chr2:38992374-38992608	MCF10A-Er-Src	breast:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:38974221..38979921-chr2:38986851..38994572,21	K562	blood:
2	chr2:38992046..38994768-chr2:39003878..39006153,3	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:
7	chr2:38992289..38994375-chr2:38996037..38998957,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000232114	TF binding region
ENSG00000152147	Chromatin interaction
ENSG00000232114	Chromatin interaction
ENSG00000115875	Chromatin interaction
ENSG00000115904	Chromatin interaction

Extended variants
information (count: 66 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs1010859	0.88[JPT][hapmap]
rs10197412	0.91[CHB][hapmap];0.94[CHD][hapmap];0.84[GIH][hapmap];0.81[ASN][1000 genomes]
rs10865143	1.00[CHB][hapmap];0.94[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs11124646	0.84[CEU][hapmap]
rs11898812	0.83[CEU][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.82[ASN][1000 genomes]
rs12472454	0.82[ASN][1000 genomes]
rs12474770	0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs12618118	1.00[CHB][hapmap];0.89[ASN][1000 genomes]
rs12621103	0.90[CHB][hapmap];0.94[CHD][hapmap];0.87[GIH][hapmap];0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs12991609	0.86[ASN][1000 genomes]
rs13024811	0.91[CHB][hapmap];0.88[CHD][hapmap];0.87[GIH][hapmap];0.83[TSI][hapmap];0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs1529625	0.91[CHB][hapmap]
rs1979143	0.96[CEU][hapmap];0.90[CHB][hapmap];0.88[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.89[TSI][hapmap];0.89[ASN][1000 genomes]
rs2037875	0.91[CHB][hapmap];0.94[CHD][hapmap];0.84[GIH][hapmap]
rs3097713	0.80[ASW][hapmap];0.91[CEU][hapmap];0.91[CHB][hapmap];0.88[CHD][hapmap];0.96[GIH][hapmap];0.88[JPT][hapmap];0.84[MEX][hapmap];0.80[MKK][hapmap];0.96[TSI][hapmap];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3097714	0.96[CEU][hapmap];0.94[CHD][hapmap];0.88[JPT][hapmap];0.85[TSI][hapmap]
rs3097716	0.86[ASN][1000 genomes]
rs3099952	0.82[AMR][1000 genomes]
rs3099961	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3099965	0.88[ASN][1000 genomes]
rs3099968	0.96[CEU][hapmap];0.90[CHB][hapmap];0.94[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.93[TSI][hapmap];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3099971	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3099975	0.82[ASN][1000 genomes]
rs3099977	0.82[ASN][1000 genomes]
rs3099980	0.86[ASN][1000 genomes]
rs3099990	0.83[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs3099992	0.82[ASN][1000 genomes]
rs3100000	1.00[JPT][hapmap]
rs3108666	0.89[ASN][1000 genomes]
rs3112142	0.81[CHB][hapmap];0.81[TSI][hapmap];0.86[ASN][1000 genomes]
rs3112143	0.82[ASN][1000 genomes]
rs3112150	0.86[ASN][1000 genomes]
rs3112152	0.89[ASN][1000 genomes]
rs3112156	0.89[ASN][1000 genomes]
rs3112159	0.88[JPT][hapmap]
rs3112161	0.89[ASN][1000 genomes]
rs3112163	1.00[JPT][hapmap]
rs3112178	0.91[CEU][hapmap];0.90[CHB][hapmap];0.88[JPT][hapmap];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3112183	1.00[CHB][hapmap];0.94[CHD][hapmap];0.87[GIH][hapmap];0.89[ASN][1000 genomes]
rs3112186	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3112188	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.89[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3112189	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3112191	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3112192	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3112194	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3112196	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3112198	0.93[ASN][1000 genomes]
rs3112204	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3112215	0.81[CEU][hapmap];0.80[TSI][hapmap]
rs3134628	0.83[CHB][hapmap];0.94[CHD][hapmap];0.84[GIH][hapmap];0.89[ASN][1000 genomes]
rs3134629	0.89[ASN][1000 genomes]
rs3134630	0.89[ASN][1000 genomes]
rs3134637	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35387882	0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs3731838	0.91[CHB][hapmap]
rs4670268	0.86[JPT][hapmap]
rs4670892	0.88[ASN][1000 genomes]
rs6544175	0.84[AMR][1000 genomes]
rs6715866	0.91[CHB][hapmap];0.89[CHD][hapmap];0.84[GIH][hapmap];0.88[ASN][1000 genomes]
rs6717670	0.87[CEU][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.85[TSI][hapmap];0.82[ASN][1000 genomes]
rs6746818	0.91[CHB][hapmap]
rs756338	0.86[ASN][1000 genomes]

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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs3112184	GALM	cis	parietal	SCAN
rs3112184	DHX57	cis	multi-tissue	Pritchard
rs3112184	DHX57	cis	cerebellum	SCAN
rs3112184	MORN2	cis	parietal	SCAN

Chromatin state (count:15 , 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	chr2:38991600-38992600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr2:38991600-38993200	Enhancers	NH-A	brain
5	chr2:38991800-38993200	Enhancers	HMEC	breast
6	chr2:38991800-38993600	Enhancers	Osteobl	bone
7	chr2:38991800-38993800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr2:38991800-38994400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr2:38992000-38993200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr2:38992000-38993200	Enhancers	HSMM	muscle
11	chr2:38992200-38993400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr2:38992200-38995200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr2:38992400-38992800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr2:38992400-38992800	Enhancers	Fetal Heart	heart
15	chr2:38992400-38992800	Enhancers	NHEK	skin

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