Variant report

Variant	rs12488904
Chromosome Location	chr3:115896878-115896879
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 64 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10804521	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10804522	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12485667	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12486465	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12496701	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap]
rs1381065	1.00[CHB][hapmap];0.94[CHD][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs1461110	0.84[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs1461112	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs1461113	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs1461115	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1461117	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1461138	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1563933	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs16824478	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs16824491	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs16824495	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17359	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17631108	0.83[EUR][1000 genomes]
rs17643878	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17698500	0.94[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs17699134	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs1920363	0.88[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.93[TSI][hapmap];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1920365	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1920367	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1920370	0.83[CEU][hapmap];0.90[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap]
rs1920375	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs1950085	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs2141628	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34424845	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41456847	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.81[YRI][hapmap]
rs4146782	0.82[CEU][hapmap];0.90[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.90[TSI][hapmap];0.85[EUR][1000 genomes]
rs4261878	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4511899	0.88[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs4560296	0.84[ASN][1000 genomes]
rs56357456	0.85[ASN][1000 genomes]
rs57196061	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs57425502	0.84[ASN][1000 genomes]
rs62269187	0.84[ASN][1000 genomes]
rs62269188	1.00[ASN][1000 genomes]
rs62269190	1.00[ASN][1000 genomes]
rs67278926	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs67551037	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6779886	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.81[YRI][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67853012	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6787788	0.90[CHB][hapmap];1.00[CHD][hapmap];0.85[ASN][1000 genomes]
rs73140910	0.85[EUR][1000 genomes]
rs73140911	0.85[EUR][1000 genomes]
rs73140912	0.85[EUR][1000 genomes]
rs73140913	0.85[EUR][1000 genomes]
rs73140921	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs73140968	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7428913	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7614089	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7639609	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1012260	chr3:115680931-115935968	Enhancers Active TSS Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	esv2756413	chr3:115721898-115908480	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
3	esv2751975	chr3:115766285-115902901	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
4	esv2755046	chr3:115818840-115942952	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
5	nsv591345	chr3:115819376-115902901	Enhancers Flanking Active TSS Weak transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
6	esv2752728	chr3:115833212-115902901	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
7	esv2751976	chr3:115867310-115903310	Enhancers Weak transcription Active TSS Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
8	esv2755082	chr3:115896250-115902901	Weak transcription Enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
9	esv2755366	chr3:115896250-115902901	Enhancers Weak transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
10	esv2755965	chr3:115896250-115902901	Enhancers Weak transcription	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:115890000-115897800	Weak transcription	Colon Smooth Muscle	Colon
2	chr3:115895800-115897600	Weak transcription	HUES64 Cell Line	embryonic stem cell
3	chr3:115896200-115897800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
4	chr3:115896200-115898000	Weak transcription	HUES48 Cell Line	embryonic stem cell
5	chr3:115896200-115898000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
6	chr3:115896400-115897000	Weak transcription	iPS-15b Cell Line	embryonic stem cell

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