Variant report

Variant	rs12502934
Chromosome Location	chr4:87014806-87014807
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 62 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10001162	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10002407	0.84[ASN][1000 genomes]
rs10009993	0.95[GIH][hapmap]
rs10023731	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10027225	0.95[ASN][1000 genomes]
rs10028075	0.88[ASW][hapmap];0.96[CEU][hapmap];0.95[GIH][hapmap];0.89[MEX][hapmap];0.86[MKK][hapmap];0.95[TSI][hapmap];0.85[YRI][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10031752	0.87[ASN][1000 genomes]
rs1010778	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11097091	0.96[CEU][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11097092	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11929863	0.88[ASN][1000 genomes]
rs11934691	0.93[EUR][1000 genomes]
rs1201	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs12502902	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12512583	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12644938	0.86[EUR][1000 genomes]
rs12644947	0.95[GIH][hapmap]
rs13103374	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13112959	0.94[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.89[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13353771	0.90[ASN][1000 genomes]
rs1436521	0.96[CEU][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1469869	0.94[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.89[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1898248	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs1898249	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs1946733	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs2118044	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2282596	0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2282597	0.84[ASN][1000 genomes]
rs2282598	0.95[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs2589506	1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs2589515	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs2589516	0.89[ASN][1000 genomes]
rs28485608	0.96[ASN][1000 genomes]
rs28865277	0.84[ASN][1000 genomes]
rs34998174	0.95[ASN][1000 genomes]
rs35823399	0.92[ASN][1000 genomes]
rs3775167	0.95[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs3775170	0.84[ASN][1000 genomes]
rs3775181	0.95[GIH][hapmap]
rs3775182	0.86[CHD][hapmap]
rs3775183	0.95[GIH][hapmap]
rs3775184	0.90[ASN][1000 genomes]
rs3775187	0.96[CEU][hapmap];0.95[GIH][hapmap];0.97[TSI][hapmap];0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4133139	0.83[AMR][1000 genomes]
rs4364253	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4482754	0.96[CEU][hapmap];0.97[GIH][hapmap];0.92[TSI][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4487330	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4501213	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6531896	0.86[EUR][1000 genomes]
rs6810413	0.96[CEU][hapmap];0.95[GIH][hapmap];0.97[TSI][hapmap];0.93[EUR][1000 genomes]
rs6822410	0.90[ASN][1000 genomes]
rs6840318	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9307015	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs958	0.95[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs9884282	0.95[CHB][hapmap];0.93[CHD][hapmap];0.96[ASN][1000 genomes]
rs9884770	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][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]
rs9995879	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.89[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1009622	chr4:86893536-87119153	Strong transcription Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv1003585	chr4:86957967-87250436	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv594761	chr4:86976413-87018488	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	esv2754254	chr4:86979147-87108510	Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv879521	chr4:86979927-87165758	Weak transcription Enhancers ZNF genes & repeats Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:87004000-87028400	Weak transcription	Stomach Smooth Muscle	stomach
2	chr4:87005000-87050400	Weak transcription	Brain Angular Gyrus	brain
3	chr4:87005400-87028200	Weak transcription	Ovary	ovary
4	chr4:87005400-87028400	Weak transcription	Fetal Stomach	stomach
5	chr4:87005600-87023000	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr4:87005600-87026200	Weak transcription	Brain Cingulate Gyrus	brain
7	chr4:87005600-87031200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
8	chr4:87005600-87035200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr4:87009200-87027400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr4:87010800-87035800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr4:87011400-87035600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr4:87011600-87023000	Weak transcription	Brain Anterior Caudate	brain
13	chr4:87011800-87028400	Weak transcription	Fetal Lung	lung
14	chr4:87012800-87015800	Weak transcription	HUES48 Cell Line	embryonic stem cell
15	chr4:87014200-87015600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr4:87014600-87015000	Weak transcription	Hela-S3	cervix
17	chr4:87014600-87015400	Weak transcription	A549	lung

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