Variant report

Variant	rs12568483
Chromosome Location	chr1:91781576-91781577
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 76 )
Associated
traits (count: 9 )

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

rs_ID	r²[population]
rs10157861	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10493845	1.00[CHB][hapmap];0.93[CHD][hapmap];0.92[JPT][hapmap];0.97[ASN][1000 genomes]
rs10801862	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs10923007	0.97[ASN][1000 genomes]
rs10923010	0.91[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs1158436	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs12093493	0.96[ASN][1000 genomes]
rs12562636	0.91[ASN][1000 genomes]
rs12563247	0.81[ASN][1000 genomes]
rs12564233	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]
rs12566254	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12566743	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12568445	0.86[AFR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1583817	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs1583818	0.89[CHD][hapmap];0.85[JPT][hapmap]
rs169472	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17131417	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17131419	0.95[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs182218	0.81[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs1823868	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs192519	0.89[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];0.86[MEX][hapmap]
rs281935	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs281956	0.82[ASN][1000 genomes]
rs281959	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs281966	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap]
rs281968	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs281979	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs281990	0.89[CHD][hapmap];0.92[JPT][hapmap];0.83[ASN][1000 genomes]
rs281992	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs281996	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs281997	0.92[JPT][hapmap];0.83[ASN][1000 genomes]
rs281998	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs282014	0.84[EUR][1000 genomes]
rs282020	0.88[ASN][1000 genomes]
rs282050	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs282053	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34390075	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4084488	0.93[AFR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4509624	0.91[AFR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4658202	0.93[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4658204	0.89[AMR][1000 genomes]
rs4658212	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4658219	0.91[AFR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4658220	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4658221	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4658222	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs56738625	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs58424833	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs59078007	0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs59973709	0.88[AMR][1000 genomes]
rs6671415	0.86[ASN][1000 genomes]
rs6678319	0.84[ASN][1000 genomes]
rs6685750	0.86[ASN][1000 genomes]
rs672449	0.80[ASN][1000 genomes]
rs681589	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs72726276	0.91[ASN][1000 genomes]
rs72970318	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72970328	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72970335	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72970337	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7417055	0.86[CHD][hapmap];0.85[JPT][hapmap]
rs7513687	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7521314	0.97[ASN][1000 genomes]
rs876761	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][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]
rs9324372	1.00[ASW][hapmap];0.87[CEU][hapmap];0.86[CHD][hapmap];0.92[GIH][hapmap];0.92[JPT][hapmap];0.91[LWK][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs9660037	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9662393	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9700732	0.82[ASN][1000 genomes]
rs9724763	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs988203	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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	nsv1006022	chr1:91768640-91831196	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	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
6	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
rs12568483	HFM1	cis	Muscle Skeletal	GTEx
rs12568483	HFM1	cis	Nerve Tibial	GTEx
rs12568483	HFM1	cis	Artery Tibial	GTEx
rs12568483	HFM1	cis	Stomach	GTEx
rs12568483	HFM1	cis	Adipose Subcutaneous	GTEx
rs12568483	HFM1	cis	Thyroid	GTEx
rs12568483	HFM1	cis	lung	GTEx
rs12568483	HFM1	cis	Esophagus Muscularis	GTEx
rs12568483	HFM1	cis	Artery Aorta	GTEx

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:91772800-91793800	Weak transcription	Left Ventricle	heart
2	chr1:91773600-91796200	Weak transcription	Fetal Kidney	kidney
3	chr1:91774800-91794400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr1:91775000-91793800	Weak transcription	Pancreas	Pancrea
5	chr1:91775200-91794000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
6	chr1:91776600-91793800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr1:91777600-91790600	Weak transcription	Fetal Brain Female	brain
8	chr1:91777600-91790600	Weak transcription	Skeletal Muscle Female	skeletal muscle
9	chr1:91777600-91790800	Weak transcription	Primary hematopoietic stem cells	blood
10	chr1:91777600-91794000	Weak transcription	Cortex derived primary cultured neurospheres	brain
11	chr1:91777800-91794600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr1:91778000-91790600	Weak transcription	Brain Germinal Matrix	brain
13	chr1:91778000-91790600	Weak transcription	Fetal Lung	lung
14	chr1:91778000-91793800	Weak transcription	Skeletal Muscle Male	skeletal muscle
15	chr1:91778000-91794000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr1:91778000-91794000	Weak transcription	Fetal Intestine Small	intestine
17	chr1:91778200-91782400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr1:91778600-91790400	Weak transcription	Fetal Stomach	stomach
19	chr1:91778600-91793800	Weak transcription	Ovary	ovary
20	chr1:91779000-91784400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr1:91779000-91793800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr1:91779800-91782400	Weak transcription	Fetal Brain Male	brain

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