Variant report

Variant	rs12502757
Chromosome Location	chr4:69018168-69018169
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:69014952..69016678-chr4:69016935..69018473,2	K562	blood:

Extended variants
information (count: 123 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:107)

rs_ID	r²[population]
rs10004522	1.00[CEU][hapmap];0.88[CHD][hapmap];0.97[GIH][hapmap];0.93[JPT][hapmap];0.92[MEX][hapmap];0.97[TSI][hapmap];0.89[EUR][1000 genomes]
rs10018943	1.00[CEU][hapmap];0.88[CHD][hapmap];0.97[GIH][hapmap];0.93[JPT][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10021559	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1079449	1.00[CEU][hapmap];0.88[CHD][hapmap];0.97[GIH][hapmap];0.93[JPT][hapmap];0.92[MEX][hapmap];0.97[TSI][hapmap];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1109360	0.80[EUR][1000 genomes]
rs11131733	0.81[EUR][1000 genomes]
rs11131735	0.87[EUR][1000 genomes]
rs11131737	0.93[JPT][hapmap];1.00[YRI][hapmap]
rs11131739	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11727567	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11731769	1.00[CEU][hapmap];1.00[JPT][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11733984	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11940802	0.87[EUR][1000 genomes]
rs11947862	0.93[EUR][1000 genomes]
rs11947869	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12501405	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12501540	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12502214	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12502946	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12503814	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12503983	1.00[CEU][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap]
rs12504120	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12504557	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12506837	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12507309	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12507767	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12645384	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12648112	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12651598	0.87[EUR][1000 genomes]
rs13115003	1.00[CEU][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap]
rs13131396	0.80[EUR][1000 genomes]
rs13132100	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13132990	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13135438	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13138038	1.00[CEU][hapmap];0.93[JPT][hapmap];0.95[YRI][hapmap]
rs13147736	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13148584	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1320264	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13435884	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1370828	1.00[CEU][hapmap];0.88[CHD][hapmap];0.97[GIH][hapmap];0.93[JPT][hapmap];0.92[MEX][hapmap];0.97[TSI][hapmap]
rs1370830	1.00[CEU][hapmap];0.88[CHD][hapmap];0.92[GIH][hapmap];0.93[JPT][hapmap];0.92[MEX][hapmap];0.97[TSI][hapmap];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1370832	1.00[CEU][hapmap];0.92[JPT][hapmap]
rs1438389	1.00[CEU][hapmap];0.93[JPT][hapmap];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1438398	0.80[EUR][1000 genomes]
rs1438439	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1438440	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1438441	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1438442	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1438443	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1438444	1.00[CEU][hapmap];0.88[CHD][hapmap];0.97[GIH][hapmap];0.93[JPT][hapmap];0.92[MEX][hapmap];0.97[TSI][hapmap];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1438445	1.00[CEU][hapmap];0.88[CHD][hapmap];0.97[GIH][hapmap];0.93[JPT][hapmap];0.92[MEX][hapmap];0.97[TSI][hapmap];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1438447	1.00[CEU][hapmap];0.92[JPT][hapmap];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1530062	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1530063	0.95[CEU][hapmap];0.88[CHD][hapmap];0.92[JPT][hapmap];0.87[TSI][hapmap];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17089005	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17089042	1.00[CEU][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap]
rs1837215	1.00[CEU][hapmap];0.93[JPT][hapmap];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1837216	0.80[EUR][1000 genomes]
rs1866327	0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1866328	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1866329	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1898644	1.00[CEU][hapmap];0.88[CHD][hapmap];0.97[GIH][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1946827	1.00[CEU][hapmap];0.93[JPT][hapmap]
rs2028249	0.81[EUR][1000 genomes]
rs2118625	1.00[CEU][hapmap];0.93[JPT][hapmap];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2164935	1.00[CEU][hapmap];0.93[JPT][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2319718	0.80[EUR][1000 genomes]
rs2319793	0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2319798	0.82[ASN][1000 genomes]
rs28535832	0.81[EUR][1000 genomes]
rs34237875	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3819257	1.00[ASW][hapmap];1.00[CEU][hapmap];0.88[CHD][hapmap];0.97[GIH][hapmap];0.93[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4317250	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4374659	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap]
rs4407557	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4538543	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4613616	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4640716	0.81[EUR][1000 genomes]
rs4860273	0.91[CEU][hapmap];0.93[JPT][hapmap]
rs4860274	0.95[CEU][hapmap];0.93[JPT][hapmap]
rs4860275	0.95[CEU][hapmap];0.92[GIH][hapmap];0.93[JPT][hapmap];0.94[TSI][hapmap]
rs4860276	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4860277	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4860278	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4860282	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4860875	0.81[EUR][1000 genomes]
rs4860897	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4860908	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59649794	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6552134	0.86[CEU][hapmap];0.87[GIH][hapmap];0.85[TSI][hapmap]
rs6552145	1.00[CEU][hapmap];0.94[CHD][hapmap];0.95[GIH][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs66943336	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6811052	1.00[CEU][hapmap];0.93[JPT][hapmap];0.95[YRI][hapmap]
rs6812743	0.91[EUR][1000 genomes]
rs6819568	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6827417	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6842578	1.00[CEU][hapmap];0.88[CHD][hapmap];0.97[GIH][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs71604558	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7435855	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7664796	0.81[EUR][1000 genomes]
rs7665583	0.81[EUR][1000 genomes]
rs7674140	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7688501	0.81[EUR][1000 genomes]
rs7688721	0.81[EUR][1000 genomes]
rs939206	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs966827	1.00[CEU][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];0.93[JPT][hapmap];0.92[MEX][hapmap];0.97[TSI][hapmap]
rs9999589	0.93[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv879219	chr4:68743032-69028913	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
2	esv2759257	chr4:68777006-69028913	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	esv1806791	chr4:68781695-69018980	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
4	esv1808905	chr4:68782651-69020080	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
5	esv1814820	chr4:68789778-69033099	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
6	esv1805370	chr4:68789778-69043722	Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
7	esv35010	chr4:68790834-69018168	Genic enhancers Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
8	esv2757060	chr4:68790864-69028913	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
9	esv1812856	chr4:68791333-69021023	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
10	nsv1008084	chr4:68797598-69482831	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
11	nsv537131	chr4:68797598-69482831	Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
12	nsv879221	chr4:68915798-69033099	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
13	esv1812438	chr4:68943858-69154222	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
14	esv1806586	chr4:68943858-69592846	ZNF genes & repeats Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
15	nsv879222	chr4:68958980-69022380	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
16	esv3400302	chr4:69008235-69034717	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12502757	GCOM2	cis	Esophagus Mucosa	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:69013000-69020400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr4:69014800-69028000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr4:69017200-69018800	Enhancers	ES-I3 Cell Line	embryonic stem cell
4	chr4:69017200-69019000	Enhancers	NHEK	skin
5	chr4:69017400-69018800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr4:69017600-69018200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr4:69017600-69018800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr4:69017600-69018800	Enhancers	Placenta Amnion	Placenta Amnion
9	chr4:69017600-69018800	Enhancers	HMEC	breast
10	chr4:69018000-69018400	Enhancers	HUES6 Cell Line	embryonic stem cell
11	chr4:69018000-69018400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin

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