Variant report

Variant	rs12490042
Chromosome Location	chr3:50434984-50434985
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:50433810..50435644-chr3:50457889..50460766,2	K562	blood:
2	chr3:50432925..50435019-chr3:50624973..50626614,2	MCF-7	breast:
3	chr3:50434095..50435683-chr3:50439071..50441884,2	K562	blood:
4	chr3:50374030..50376219-chr3:50433373..50435985,2	MCF-7	breast:
5	chr3:50423026..50425468-chr3:50433598..50435342,2	K562	blood:

Variant related genes	Relation type
ENSG00000068028	Chromatin interaction

Extended variants
information (count: 86 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs1107265	0.94[CEU][hapmap];0.86[JPT][hapmap];0.90[EUR][1000 genomes]
rs11130250	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12492113	0.87[CEU][hapmap];0.93[AMR][1000 genomes]
rs12494849	0.83[CEU][hapmap]
rs13087550	1.00[CEU][hapmap];0.83[CHB][hapmap];0.95[JPT][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13091933	0.83[CEU][hapmap]
rs13094336	0.81[CEU][hapmap]
rs13099869	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1467913	0.83[CEU][hapmap]
rs1467914	0.83[CEU][hapmap]
rs2027854	0.93[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2073496	0.90[EUR][1000 genomes]
rs2236950	0.87[AMR][1000 genomes]
rs2236953	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2236954	0.94[CEU][hapmap];0.80[JPT][hapmap];0.90[EUR][1000 genomes]
rs2236955	0.94[CEU][hapmap];0.83[JPT][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2236956	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2236957	0.94[CEU][hapmap];0.81[JPT][hapmap];0.84[EUR][1000 genomes]
rs2236958	1.00[CEU][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2236959	0.94[CEU][hapmap]
rs2236961	1.00[CEU][hapmap];0.95[JPT][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2236962	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2236963	1.00[CEU][hapmap];0.95[JPT][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2236964	0.94[CEU][hapmap];0.81[JPT][hapmap];0.86[EUR][1000 genomes]
rs2236965	0.94[CEU][hapmap];0.81[JPT][hapmap];0.86[EUR][1000 genomes]
rs2236967	1.00[CEU][hapmap];0.95[JPT][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2236968	1.00[CEU][hapmap];0.82[CHB][hapmap];0.95[JPT][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2236971	1.00[CEU][hapmap];0.82[CHB][hapmap];0.95[JPT][hapmap];0.99[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2236973	0.94[CEU][hapmap];0.81[JPT][hapmap];0.81[EUR][1000 genomes]
rs2236975	1.00[CEU][hapmap];0.82[CHB][hapmap];0.95[JPT][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2236979	0.94[CEU][hapmap];0.81[JPT][hapmap]
rs2236981	0.84[EUR][1000 genomes]
rs2236983	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2236984	0.94[CEU][hapmap];0.81[JPT][hapmap]
rs2236987	0.94[CEU][hapmap]
rs2236988	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2282752	0.94[CEU][hapmap];0.83[JPT][hapmap];0.84[EUR][1000 genomes]
rs2282753	0.94[CEU][hapmap];0.86[JPT][hapmap];0.90[EUR][1000 genomes]
rs2282754	0.94[CEU][hapmap];0.86[JPT][hapmap];0.90[EUR][1000 genomes]
rs2282756	1.00[CEU][hapmap];0.95[JPT][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2282758	1.00[CEU][hapmap];0.83[CHB][hapmap];0.95[JPT][hapmap];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2282760	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2298955	0.94[CEU][hapmap];0.86[JPT][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs34762184	0.88[CEU][hapmap]
rs35986136	0.88[CEU][hapmap]
rs4688719	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4688720	0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs628081	0.84[CEU][hapmap]
rs6446206	0.86[EUR][1000 genomes]
rs6786523	0.83[CEU][hapmap]
rs6787890	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6788459	0.93[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6792502	0.84[CEU][hapmap]
rs6807916	0.89[CEU][hapmap]
rs71326932	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs734767	0.94[CEU][hapmap];0.86[JPT][hapmap];0.90[EUR][1000 genomes]
rs743756	0.94[CEU][hapmap];0.81[JPT][hapmap];0.81[EUR][1000 genomes]
rs743757	0.94[CEU][hapmap];0.81[JPT][hapmap];0.81[EUR][1000 genomes]
rs743857	0.94[CEU][hapmap];0.81[JPT][hapmap]
rs762895	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs762897	1.00[CEU][hapmap];0.83[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs762898	1.00[CEU][hapmap];0.95[JPT][hapmap];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs763030	0.84[CEU][hapmap]
rs8180034	0.96[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs916217	1.00[CEU][hapmap];0.82[CHB][hapmap];0.95[JPT][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs929047	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9835537	0.94[CEU][hapmap];0.80[JPT][hapmap];0.84[EUR][1000 genomes]
rs9867588	0.88[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:18 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv523662	chr3:50144951-50584999	Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	101 gene(s)	inside rSNPs	diseases
2	esv1821728	chr3:50156142-50657253	Strong transcription Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	109 gene(s)	inside rSNPs	diseases
3	esv1793751	chr3:50157364-50476363	Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
4	esv1828162	chr3:50157364-50506151	Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
5	nsv470561	chr3:50158774-50584999	Flanking Active TSS Enhancers Weak transcription Genic enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	99 gene(s)	inside rSNPs	diseases
6	nsv876770	chr3:50158774-50609624	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
7	nsv1001993	chr3:50187646-50640808	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
8	nsv460531	chr3:50247824-50436827	Strong transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
9	nsv590255	chr3:50247824-50436827	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
10	nsv876772	chr3:50255305-50436827	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
11	nsv876774	chr3:50302830-50436827	Enhancers Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
12	nsv876773	chr3:50302830-50480131	Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
13	nsv834693	chr3:50302830-50507964	Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
14	nsv876775	chr3:50324672-50504896	Flanking Active TSS Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
15	esv3584502	chr3:50368278-50659741	Strong transcription Bivalent/Poised TSS Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
16	nsv432419	chr3:50388396-50637496	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
17	nsv876778	chr3:50413707-50465518	Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region	13 gene(s)	inside rSNPs	diseases
18	nsv590271	chr3:50420554-50436716	Weak transcription Bivalent Enhancer Enhancers Genic enhancers Bivalent/Poised TSS Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats	Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:50426400-50438000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr3:50431000-50435400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
3	chr3:50431200-50442000	Weak transcription	Skeletal Muscle Male	skeletal muscle
4	chr3:50433600-50439600	Weak transcription	Spleen	Spleen
5	chr3:50434200-50435000	Weak transcription	Fetal Muscle Leg	muscle
6	chr3:50434200-50435200	Enhancers	Fetal Muscle Trunk	muscle
7	chr3:50434400-50437800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr3:50434600-50435400	Enhancers	Brain Germinal Matrix	brain

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