Variant report

Variant	rs6753859
Chromosome Location	chr2:172754554-172754555
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CUX1	chr2:172754291-172754627	K562	blood:	n/a	n/a
2	FOXA1	chr2:172754142-172754596	HepG2	liver:	n/a	n/a
3	MEF2A	chr2:172754215-172754591	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:172749510..172752866-chr2:172752874..172756053,4	K562	blood:

Variant related genes	Relation type
SLC25A12	TF binding region
ENSG00000115840	Chromatin interaction

Extended variants
information (count: 120 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:116)

rs_ID	r²[population]
rs10177679	1.00[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10179020	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10184770	0.80[ASN][1000 genomes]
rs10185633	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10191399	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10196521	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.90[TSI][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10201520	0.84[EUR][1000 genomes]
rs1022358	1.00[CHB][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap]
rs10432474	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10439296	0.94[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap]
rs10930493	0.82[ASN][1000 genomes]
rs10930497	1.00[CEU][hapmap]
rs10930501	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1105264	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11676484	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.90[TSI][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11677573	0.86[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.84[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs11683436	0.85[AMR][1000 genomes]
rs11692418	1.00[JPT][hapmap]
rs11887208	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11903123	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11903410	0.85[AMR][1000 genomes]
rs12464262	0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs12467010	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12471160	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12473516	0.85[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.90[TSI][hapmap];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12478189	0.81[ASN][1000 genomes]
rs12479374	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12617265	0.88[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap]
rs12619137	0.94[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap]
rs12692979	0.94[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap]
rs13012103	0.84[EUR][1000 genomes]
rs13017988	0.94[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs13031370	0.85[AMR][1000 genomes]
rs13399316	0.94[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1400816	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1443700	0.94[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap]
rs1515812	0.86[ASN][1000 genomes]
rs1517678	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1543168	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1554165	0.86[ASN][1000 genomes]
rs1607253	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs16859721	0.86[ASN][1000 genomes]
rs17580984	0.86[ASN][1000 genomes]
rs17581715	1.00[CEU][hapmap]
rs17614989	0.86[ASN][1000 genomes]
rs17615013	0.86[ASN][1000 genomes]
rs1850031	0.86[ASN][1000 genomes]
rs1878583	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.90[TSI][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1982288	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.90[TSI][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1996425	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2028670	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.90[TSI][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2028671	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.90[TSI][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2028672	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2037164	0.86[ASN][1000 genomes]
rs2056202	0.94[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap]
rs2176466	1.00[JPT][hapmap]
rs2292813	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.90[TSI][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2292814	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.90[TSI][hapmap];0.81[EUR][1000 genomes]
rs2357064	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs2357206	0.94[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap]
rs2357207	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2357208	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28372952	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.90[TSI][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs312917	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.90[TSI][hapmap];0.80[ASN][1000 genomes]
rs3770443	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3770444	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3770453	0.86[CHB][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap]
rs3770457	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3791343	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3821092	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3821094	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.90[TSI][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3821096	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.90[TSI][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4324292	0.88[JPT][hapmap]
rs4507064	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4668417	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.90[TSI][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4668419	0.80[ASN][1000 genomes]
rs58565148	0.86[ASN][1000 genomes]
rs60706248	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6433313	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.90[TSI][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6433315	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.90[TSI][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6433316	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6433317	0.94[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap]
rs6433318	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.90[TSI][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6433322	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];0.88[JPT][hapmap];0.88[MEX][hapmap];0.90[TSI][hapmap];0.85[AMR][1000 genomes]
rs6707142	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.90[TSI][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6711813	0.81[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap]
rs6714214	1.00[CEU][hapmap];0.86[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.90[TSI][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6726050	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6733123	0.83[AMR][1000 genomes]
rs6736159	0.94[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap]
rs6740705	0.94[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap]
rs6742905	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6753551	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6757680	0.83[GIH][hapmap];0.88[JPT][hapmap]
rs6758494	1.00[JPT][hapmap]
rs6760680	1.00[JPT][hapmap]
rs718936	1.00[CEU][hapmap]
rs7340516	0.94[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap]
rs7371503	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs7371631	0.85[AMR][1000 genomes]
rs7560031	1.00[CEU][hapmap]
rs7574711	0.80[ASN][1000 genomes]
rs7579509	0.82[CEU][hapmap];1.00[JPT][hapmap]
rs7580132	0.82[CEU][hapmap];0.94[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap]
rs7580232	0.94[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap]
rs7583860	0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs7588025	1.00[JPT][hapmap]
rs7588351	0.86[ASN][1000 genomes]
rs7594478	0.94[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap]
rs7597525	0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7598232	0.85[AMR][1000 genomes]
rs7604933	0.83[EUR][1000 genomes]
rs925881	0.85[CHB][hapmap];0.94[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap]
rs9287948	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs949548	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.90[TSI][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs970948	1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.82[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	nsv834457	chr2:172564939-172770901	Strong transcription Genic enhancers Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv875410	chr2:172693780-172896587	Weak transcription Strong transcription Active TSS Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
3	nsv875411	chr2:172693780-172942448	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
4	nsv536037	chr2:172745597-172780616	Flanking Active TSS Strong transcription Active TSS Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:172751600-172754800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chr2:172753600-172755200	Enhancers	Breast Myoepithelial Primary Cells	Breast
3	chr2:172754000-172754600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr2:172754000-172754600	Enhancers	HepG2	liver
5	chr2:172754000-172754800	Enhancers	Skeletal Muscle Male	skeletal muscle
6	chr2:172754200-172754600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr2:172754200-172754600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr2:172754200-172754600	Enhancers	Aorta	Aorta
9	chr2:172754400-172754600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr2:172754400-172754600	Enhancers	Liver	Liver
11	chr2:172754400-172759600	Weak transcription	Osteobl	bone

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