Variant report

Variant	rs12022870
Chromosome Location	chr1:152846400-152846401
allele	A/G
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	JUND	chr1:152845760-152846580	SK-N-SH	brain:	n/a	n/a
2	GATA3	chr1:152845752-152846470	SK-N-SH	brain:	n/a	n/a
3	NFIC	chr1:152845766-152846410	SK-N-SH	brain:	n/a	n/a
4	TEAD4	chr1:152845948-152846488	SK-N-SH	brain:	n/a	n/a
5	FOS	chr1:152846020-152846436	MCF10A-Er-Src	breast:	n/a	n/a
6	FOSL2	chr1:152845791-152846502	SK-N-SH	brain:	n/a	n/a
7	PBX3	chr1:152845717-152846454	SK-N-SH	brain:	n/a	n/a
8	JUND	chr1:152845821-152846500	SK-N-SH	brain:	n/a	n/a
9	EP300	chr1:152845730-152846511	SK-N-SH	brain:	n/a	n/a
10	PBX3	chr1:152845822-152846407	SK-N-SH	brain:	n/a	n/a
11	GATA3	chr1:152845797-152846408	SK-N-SH	brain:	n/a	n/a
12	TCF12	chr1:152845801-152846486	SK-N-SH	brain:	n/a	n/a
13	MEF2A	chr1:152845939-152846442	SK-N-SH	brain:	n/a	n/a
14	TCF12	chr1:152845773-152846604	SK-N-SH	brain:	n/a	n/a

Variant related genes	Relation type
SMCP	TF binding region

Extended variants
information (count: 83 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs10494280	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10494288	1.00[EUR][1000 genomes]
rs10888521	1.00[EUR][1000 genomes]
rs11205126	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11205128	0.90[CHB][hapmap];0.85[JPT][hapmap];0.92[ASN][1000 genomes]
rs11205129	0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs11205130	1.00[EUR][1000 genomes]
rs11205131	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs11205147	1.00[EUR][1000 genomes]
rs11801996	0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs11806470	1.00[EUR][1000 genomes]
rs12021601	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12022319	0.90[CHB][hapmap];0.81[JPT][hapmap];0.82[ASN][1000 genomes]
rs12022349	0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs12023643	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12024694	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs12028228	0.81[ASN][1000 genomes]
rs12029192	1.00[EUR][1000 genomes]
rs12032522	1.00[EUR][1000 genomes]
rs12034091	1.00[CEU][hapmap]
rs12036697	1.00[EUR][1000 genomes]
rs12037754	1.00[CEU][hapmap]
rs12047099	1.00[EUR][1000 genomes]
rs12047630	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs12047888	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12048655	0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12239808	1.00[CEU][hapmap];0.95[JPT][hapmap]
rs12239812	1.00[CEU][hapmap];0.91[JPT][hapmap];1.00[EUR][1000 genomes]
rs12239814	1.00[CEU][hapmap];0.95[JPT][hapmap]
rs1415973	1.00[EUR][1000 genomes]
rs16834715	0.99[ASN][1000 genomes]
rs16834728	0.90[CHB][hapmap];0.82[JPT][hapmap];0.80[ASN][1000 genomes]
rs16834734	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs16834746	1.00[CEU][hapmap];0.95[JPT][hapmap];1.00[EUR][1000 genomes]
rs16834751	1.00[CEU][hapmap]
rs16834838	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs16834871	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs1974141	1.00[EUR][1000 genomes]
rs1995307	1.00[CEU][hapmap]
rs2339383	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2339501	1.00[CEU][hapmap]
rs2879485	1.00[CEU][hapmap];0.95[JPT][hapmap]
rs36090881	1.00[EUR][1000 genomes]
rs3737861	0.90[CHB][hapmap];0.82[JPT][hapmap];0.80[ASN][1000 genomes]
rs3737862	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4240863	1.00[CEU][hapmap];0.81[YRI][hapmap];0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4240864	1.00[EUR][1000 genomes]
rs4363387	0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs4845325	1.00[CEU][hapmap]
rs4845328	1.00[EUR][1000 genomes]
rs4845489	1.00[ASN][1000 genomes]
rs4845490	0.91[CHB][hapmap];0.83[JPT][hapmap];0.82[ASN][1000 genomes]
rs4845491	0.90[CHB][hapmap];0.82[JPT][hapmap];0.82[ASN][1000 genomes]
rs4845492	0.90[CHB][hapmap];0.82[JPT][hapmap];0.80[ASN][1000 genomes]
rs4845494	0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs4845498	1.00[EUR][1000 genomes]
rs58021079	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58290373	1.00[EUR][1000 genomes]
rs59837747	1.00[EUR][1000 genomes]
rs60500053	1.00[EUR][1000 genomes]
rs60566199	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs61482767	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61491150	1.00[EUR][1000 genomes]
rs6668295	1.00[EUR][1000 genomes]
rs6696961	0.81[AFR][1000 genomes]
rs73006590	0.99[ASN][1000 genomes]
rs7542656	0.90[ASN][1000 genomes]
rs7552416	1.00[CEU][hapmap];0.81[YRI][hapmap]
rs7553755	0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs7556490	0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2757755	chr1:152472839-152898153	Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
2	esv2758970	chr1:152472839-152898153	ZNF genes & repeats Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
3	nsv427786	chr1:152572990-152898153	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
4	nsv1013433	chr1:152619305-153262215	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Active TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
5	nsv535170	chr1:152619305-153262215	Enhancers Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
6	nsv1001834	chr1:152648853-153279143	Enhancers Weak transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	44 gene(s)	inside rSNPs	diseases
7	nsv547899	chr1:152672005-153245082	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases
8	nsv999918	chr1:152749733-152861866	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
9	nsv1009885	chr1:152762750-152851273	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
10	nsv1000159	chr1:152809514-152853766	Weak transcription Enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
11	nsv1008447	chr1:152811171-152853748	Enhancers Weak transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
12	esv2761937	chr1:152811183-152853760	Weak transcription Enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
13	nsv831592	chr1:152815054-152997162	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:152844000-152850800	Weak transcription	NHEK	skin
2	chr1:152844200-152846400	Weak transcription	Fetal Stomach	stomach
3	chr1:152845400-152846400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr1:152845600-152846600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr1:152845800-152846400	Enhancers	NHLF	lung
6	chr1:152845800-152846800	Enhancers	Muscle Satellite Cultured Cells	--
7	chr1:152846000-152846400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr1:152846000-152846400	Enhancers	Osteobl	bone
9	chr1:152846000-152846600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr1:152846000-152846600	Enhancers	HMEC	breast
11	chr1:152846400-152847000	Enhancers	Fetal Stomach	stomach
12	chr1:152846400-152849800	Weak transcription	NHLF	lung
13	chr1:152846400-152850800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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