Variant report

Variant	rs4658219
Chromosome Location	chr1:91844815-91844816
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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

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

rs_ID	r²[population]
rs10157861	0.83[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs10493845	1.00[CHB][hapmap];0.86[CHD][hapmap];0.83[ASN][1000 genomes]
rs10801862	1.00[CHB][hapmap];0.86[CHD][hapmap];0.83[JPT][hapmap];0.83[ASN][1000 genomes]
rs10923007	0.83[ASN][1000 genomes]
rs10923010	0.91[CHB][hapmap];0.83[JPT][hapmap];0.83[ASN][1000 genomes]
rs1158436	1.00[CHB][hapmap];0.83[JPT][hapmap];0.82[ASN][1000 genomes]
rs12093493	0.82[ASN][1000 genomes]
rs12564233	1.00[ASW][hapmap];1.00[CEU][hapmap];0.92[GIH][hapmap];0.83[JPT][hapmap];0.91[LWK][hapmap];0.83[MKK][hapmap];0.86[TSI][hapmap];0.90[YRI][hapmap];0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12566254	0.83[AFR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12566743	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12568445	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12568483	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.92[GIH][hapmap];0.83[JPT][hapmap];0.91[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1583817	1.00[CHB][hapmap];0.89[CHD][hapmap];0.83[JPT][hapmap]
rs1583818	0.83[CHD][hapmap]
rs169472	0.91[EUR][1000 genomes]
rs17131417	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.92[GIH][hapmap];0.83[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17131419	0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs182218	0.81[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs1823868	0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs192519	0.83[CHD][hapmap];0.92[GIH][hapmap];0.83[ASN][1000 genomes]
rs281935	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.92[GIH][hapmap];0.83[JPT][hapmap];0.83[LWK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs281959	1.00[CHB][hapmap];0.92[CHD][hapmap];0.83[JPT][hapmap]
rs281966	1.00[CHB][hapmap];0.89[CHD][hapmap];0.83[JPT][hapmap]
rs281968	1.00[CHB][hapmap];0.92[CHD][hapmap];0.83[JPT][hapmap]
rs281979	1.00[CHB][hapmap];0.92[CHD][hapmap];0.83[JPT][hapmap];0.83[ASN][1000 genomes]
rs281990	0.83[CHD][hapmap];0.83[JPT][hapmap]
rs281992	1.00[CHB][hapmap];0.92[CHD][hapmap];0.83[JPT][hapmap];0.83[ASN][1000 genomes]
rs281996	1.00[CHB][hapmap];0.89[CHD][hapmap];0.83[JPT][hapmap];0.82[ASN][1000 genomes]
rs281998	1.00[CHB][hapmap];0.83[JPT][hapmap];0.83[ASN][1000 genomes]
rs282014	0.83[ASN][1000 genomes]
rs282020	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs282050	0.91[EUR][1000 genomes]
rs282053	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34390075	0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4084488	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4509624	0.91[AFR][1000 genomes];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4658212	0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4658217	0.86[AMR][1000 genomes]
rs4658220	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.92[GIH][hapmap];0.83[JPT][hapmap];1.00[LWK][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4658221	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];0.92[GIH][hapmap];0.83[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4658222	1.00[CEU][hapmap];0.83[JPT][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56738625	0.83[AFR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs58424833	0.83[AFR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs59078007	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs681589	1.00[CHB][hapmap];0.92[CHD][hapmap];0.83[JPT][hapmap]
rs72970318	0.83[AFR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72970328	0.83[AFR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72970335	0.83[AFR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72970337	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7513687	0.91[AFR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7521314	0.83[ASN][1000 genomes]
rs876761	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.92[GIH][hapmap];0.83[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9324372	1.00[ASW][hapmap];0.87[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9660037	0.83[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs9662393	0.87[EUR][1000 genomes]
rs9724763	0.91[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs988203	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];0.84[GIH][hapmap];0.83[JPT][hapmap];1.00[TSI][hapmap];0.82[EUR][1000 genomes];0.97[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	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	esv1800676	chr1:91722083-91854389	Enhancers Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	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
4	nsv871685	chr1:91774458-91849219	Strong transcription ZNF genes & repeats Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	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
rs4658219	HFM1	cis	Adipose Subcutaneous	GTEx
rs4658219	HFM1	cis	Artery Aorta	GTEx
rs4658219	HFM1	cis	Artery Tibial	GTEx
rs4658219	HFM1	cis	Muscle Skeletal	GTEx
rs4658219	HFM1	cis	Stomach	GTEx
rs4658219	HFM1	cis	Esophagus Muscularis	GTEx
rs4658219	HFM1	cis	Nerve Tibial	GTEx
rs4658219	HFM1	cis	lung	GTEx
rs4658219	HFM1	cis	Thyroid	GTEx

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:91819400-91845200	Weak transcription	Skeletal Muscle Male	skeletal muscle
2	chr1:91822800-91849000	Weak transcription	Rectal Smooth Muscle	rectum
3	chr1:91824800-91852600	Weak transcription	Skeletal Muscle Female	skeletal muscle
4	chr1:91825000-91852600	Weak transcription	Stomach Smooth Muscle	stomach
5	chr1:91829800-91852600	Weak transcription	Brain Germinal Matrix	brain
6	chr1:91832000-91852600	Weak transcription	Fetal Heart	heart
7	chr1:91833000-91852600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr1:91833000-91852600	Weak transcription	Fetal Stomach	stomach
9	chr1:91836800-91852600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
10	chr1:91837200-91846000	Weak transcription	Psoas Muscle	Psoas
11	chr1:91839000-91852600	Weak transcription	Fetal Intestine Large	intestine
12	chr1:91839800-91846600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
13	chr1:91840400-91852600	Weak transcription	Fetal Kidney	kidney
14	chr1:91840600-91852600	Weak transcription	Ovary	ovary
15	chr1:91840800-91852600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr1:91840800-91852600	Weak transcription	Fetal Brain Male	brain
17	chr1:91840800-91852600	Weak transcription	Fetal Lung	lung
18	chr1:91841200-91847400	Weak transcription	Left Ventricle	heart
19	chr1:91841400-91852600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr1:91843400-91852600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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