Variant report

Variant	rs3112189
Chromosome Location	chr2:38995380-38995381
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:38992665..38995431-chr2:39003330..39006208,3	K562	blood:
2	chr2:38993209..38995928-chr2:39007575..39009225,2	MCF-7	breast:
3	chr2:38989424..38992394-chr2:38992856..38995438,2	K562	blood:
4	chr2:38991194..38992863-chr2:38993787..38996027,2	MCF-7	breast:
5	chr2:38976319..38979796-chr2:38988969..38996616,16	MCF-7	breast:
6	chr2:38973912..38980240-chr2:38989822..38999883,17	MCF-7	breast:
7	chr2:38977122..38981176-chr2:38994666..38999219,6	K562	blood:

Variant related genes	Relation type
ENSG00000115875	Chromatin interaction
ENSG00000152147	Chromatin interaction
ENSG00000227238	Chromatin interaction

Extended variants
information (count: 66 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs1010859	0.88[JPT][hapmap]
rs10197412	0.91[CHB][hapmap];0.81[ASN][1000 genomes]
rs10865143	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs11124646	0.84[CEU][hapmap]
rs11898812	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][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];0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs12991609	0.86[ASN][1000 genomes]
rs13024811	0.91[CHB][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];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs2037875	0.91[CHB][hapmap]
rs3097713	0.91[CEU][hapmap];0.91[CHB][hapmap];0.88[JPT][hapmap];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3097714	0.96[CEU][hapmap];0.88[JPT][hapmap]
rs3097716	0.86[ASN][1000 genomes]
rs3099952	0.82[AMR][1000 genomes]
rs3099961	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3099965	0.88[ASN][1000 genomes]
rs3099968	0.96[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3099971	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[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];0.83[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];0.86[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	0.87[CEU][hapmap];0.90[CHB][hapmap];0.88[JPT][hapmap];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3112183	1.00[CHB][hapmap];0.89[ASN][1000 genomes]
rs3112184	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]
rs3112186	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3112188	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[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];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3112192	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3112194	0.83[AMR][1000 genomes];0.98[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]
rs3134628	0.83[CHB][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];0.80[YRI][hapmap];0.92[AMR][1000 genomes];0.89[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];0.88[ASN][1000 genomes]
rs6717670	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs6746818	0.92[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

No data

Chromatin state (count:10 , 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	chr2:38993400-38998800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr2:38993600-38999000	Weak transcription	Osteobl	bone
4	chr2:38993800-38997200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr2:38994200-38995400	Enhancers	HepG2	liver
6	chr2:38994200-38995600	Enhancers	Liver	Liver
7	chr2:38994200-38998200	Enhancers	Fetal Heart	heart
8	chr2:38994600-38998800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr2:38994600-39004600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr2:38995200-38998800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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