Variant report

Variant	rs12564233
Chromosome Location	chr1:91865122-91865123
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:91862177..91865851-chr1:91867476..91870440,3	K562	blood:
2	chr1:91747922..91748906-chr1:91864564..91866357,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000162669	Chromatin interaction

Extended variants
information (count: 62 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs10157861	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10493845	0.92[JPT][hapmap];0.81[ASN][1000 genomes]
rs10801862	0.86[CHD][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs10923006	0.81[JPT][hapmap]
rs10923007	0.81[ASN][1000 genomes]
rs10923010	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs1158436	1.00[JPT][hapmap]
rs12566254	0.83[AFR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12566743	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12568445	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12568483	1.00[ASW][hapmap];1.00[CEU][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.84[MKK][hapmap];0.86[TSI][hapmap];0.90[YRI][hapmap];0.82[AFR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1583817	0.83[CHD][hapmap];1.00[JPT][hapmap]
rs1583818	0.83[CHD][hapmap];0.92[JPT][hapmap]
rs169472	0.97[EUR][1000 genomes]
rs17131417	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.84[MKK][hapmap];0.86[TSI][hapmap];0.90[YRI][hapmap];0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17131419	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs182218	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs1823868	1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs192519	0.83[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs281935	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.80[MKK][hapmap];0.86[TSI][hapmap];0.81[YRI][hapmap];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs281959	0.86[CHD][hapmap];1.00[JPT][hapmap]
rs281966	0.83[CHD][hapmap];1.00[JPT][hapmap]
rs281968	0.86[CHD][hapmap];1.00[JPT][hapmap]
rs281979	0.86[CHD][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs281990	0.83[CHD][hapmap];1.00[JPT][hapmap]
rs281992	0.86[CHD][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs281996	0.83[CHD][hapmap];1.00[JPT][hapmap]
rs281997	1.00[JPT][hapmap]
rs281998	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs282014	0.96[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs282020	0.94[ASN][1000 genomes]
rs282050	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs282053	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34390075	1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4084488	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4509624	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4658202	0.81[EUR][1000 genomes]
rs4658212	1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4658219	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4658220	1.00[ASW][hapmap];1.00[CEU][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.92[MKK][hapmap];0.86[TSI][hapmap];0.90[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4658221	1.00[ASW][hapmap];1.00[CEU][hapmap];0.86[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.84[MKK][hapmap];0.85[TSI][hapmap];0.90[YRI][hapmap];0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4658222	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56738625	0.83[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs58424833	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs59078007	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs681589	0.86[CHD][hapmap];1.00[JPT][hapmap]
rs72970318	0.83[AFR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72970328	0.83[AFR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72970335	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72970337	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7417055	0.92[JPT][hapmap]
rs7513687	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7521314	0.81[ASN][1000 genomes]
rs876761	1.00[ASW][hapmap];1.00[CEU][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.84[MKK][hapmap];0.86[TSI][hapmap];0.90[YRI][hapmap];0.82[AFR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9324372	1.00[ASW][hapmap];0.86[CEU][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MKK][hapmap];0.86[TSI][hapmap];0.90[YRI][hapmap];0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9660037	0.90[EUR][1000 genomes]
rs9662393	0.93[EUR][1000 genomes]
rs9724763	0.82[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs988203	1.00[CEU][hapmap];0.86[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949516	chr1:91644418-92109261	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	esv1796351	chr1:91722083-91872374	Active TSS Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers ZNF genes & repeats Weak transcription Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
3	nsv546806	chr1:91780408-91875505	Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Enhancers ZNF genes & repeats Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs12564233	HFM1	cis	Muscle Skeletal	GTEx
rs12564233	HFM1	cis	lung	GTEx
rs12564233	HFM1	cis	Esophagus Muscularis	GTEx
rs12564233	HFM1	cis	Stomach	GTEx
rs12564233	HFM1	cis	Artery Aorta	GTEx
rs12564233	HFM1	cis	Nerve Tibial	GTEx
rs12564233	HFM1	cis	Artery Tibial	GTEx
rs12564233	HFM1	cis	Thyroid	GTEx
rs12564233	HFM1	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:91853200-91866800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr1:91853200-91869200	Weak transcription	HUES6 Cell Line	embryonic stem cell
3	chr1:91853200-91869200	Weak transcription	Stomach Smooth Muscle	stomach
4	chr1:91853200-91869400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr1:91853200-91869600	Weak transcription	Skeletal Muscle Female	skeletal muscle
6	chr1:91857800-91866800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr1:91861600-91869400	Weak transcription	Primary hematopoietic stem cells	blood
8	chr1:91863600-91869400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr1:91863600-91869600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr1:91863800-91865800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr1:91864000-91866800	Weak transcription	Colon Smooth Muscle	Colon
12	chr1:91864200-91869400	Weak transcription	Cortex derived primary cultured neurospheres	brain
13	chr1:91864200-91869600	Weak transcription	Rectal Smooth Muscle	rectum
14	chr1:91864400-91865800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr1:91864400-91869400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr1:91865000-91869600	Weak transcription	Fetal Muscle Trunk	muscle

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