Variant report

Variant	rs5012561
Chromosome Location	chr2:55742032-55742033
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:55659643..55661172-chr2:55741607..55744341,2	MCF-7	breast:
2	chr2:55741679..55743940-chr2:55745074..55747931,2	K562	blood:
3	chr2:55495061..55497055-chr2:55740247..55742964,2	MCF-7	breast:
4	chr2:55740884..55742822-chr2:55843227..55845306,2	MCF-7	breast:
5	chr2:55735103..55738045-chr2:55741187..55743259,2	K562	blood:
6	chr2:55740661..55742965-chr2:55745170..55747849,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000085760	Chromatin interaction
ENSG00000272606	Chromatin interaction
ENSG00000163001	Chromatin interaction
ENSG00000138041	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs1013138	0.82[JPT][hapmap]
rs12617627	0.90[CHB][hapmap];0.89[JPT][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs12618859	0.83[JPT][hapmap];0.96[YRI][hapmap]
rs12619903	0.82[CEU][hapmap];0.92[YRI][hapmap]
rs12986444	0.84[AFR][1000 genomes]
rs12986587	0.81[CHB][hapmap];0.83[JPT][hapmap];0.81[ASN][1000 genomes]
rs12992408	0.90[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs12992827	0.82[ASN][1000 genomes]
rs12993624	0.89[JPT][hapmap];0.88[YRI][hapmap];0.82[AFR][1000 genomes]
rs12993642	0.82[ASN][1000 genomes]
rs12998664	0.84[JPT][hapmap]
rs12998780	0.80[JPT][hapmap]
rs12998925	0.81[EUR][1000 genomes]
rs12999506	0.83[AFR][1000 genomes]
rs12999680	0.89[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs12999966	0.82[CEU][hapmap];0.92[YRI][hapmap]
rs13001425	0.84[JPT][hapmap];0.87[YRI][hapmap]
rs13005678	0.99[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs13006502	0.91[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs13009239	0.87[ASN][1000 genomes]
rs13009447	0.83[CHB][hapmap];0.83[JPT][hapmap];0.86[YRI][hapmap]
rs13009906	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13010217	0.89[JPT][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes]
rs13014898	0.86[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs13015018	0.86[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs13015030	0.86[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs13015744	0.81[JPT][hapmap]
rs13021958	1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs13025331	0.89[JPT][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes]
rs13027095	0.82[AFR][1000 genomes]
rs13027853	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13032503	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1318672	0.91[CHB][hapmap];0.95[JPT][hapmap];0.88[YRI][hapmap];0.87[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs17737233	0.84[JPT][hapmap]
rs1822513	0.81[CHB][hapmap];0.84[JPT][hapmap];0.87[YRI][hapmap]
rs2291336	0.84[JPT][hapmap]
rs34013926	0.87[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs34143512	0.91[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs34679603	0.80[ASN][1000 genomes]
rs35189503	0.80[ASN][1000 genomes]
rs3791654	0.89[JPT][hapmap];0.92[YRI][hapmap];0.81[AFR][1000 genomes]
rs3828238	0.84[JPT][hapmap]
rs4312532	0.86[CEU][hapmap];0.95[JPT][hapmap];0.80[EUR][1000 genomes]
rs4322879	0.96[CEU][hapmap];0.81[JPT][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs56122729	0.83[ASN][1000 genomes]
rs66545054	0.89[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs6737995	0.84[JPT][hapmap];0.96[YRI][hapmap];0.83[AFR][1000 genomes]
rs6757006	0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7575170	0.81[CEU][hapmap];0.85[JPT][hapmap];0.92[YRI][hapmap]
rs8080	0.91[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1006170	chr2:55530179-55809251	Strong transcription Weak transcription Bivalent/Poised TSS Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv520581	chr2:55622825-55903016	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
3	nsv531374	chr2:55653723-56299784	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
4	nsv874160	chr2:55713102-55828974	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
5	nsv525434	chr2:55716650-55841640	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
6	nsv834080	chr2:55741036-55927928	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55739000-55745600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
2	chr2:55739000-55745800	Weak transcription	Brain Angular Gyrus	brain
3	chr2:55739000-55745800	Weak transcription	Thymus	Thymus
4	chr2:55739000-55745800	Weak transcription	NHEK	skin
5	chr2:55741800-55745800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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