Variant report

Variant	rs204304
Chromosome Location	chr1:91779203-91779204
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 31 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs1034499	1.00[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs10801849	0.95[CHB][hapmap];0.89[CHD][hapmap];0.86[JPT][hapmap]
rs10801851	0.87[ASW][hapmap];0.87[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.91[GIH][hapmap];0.86[JPT][hapmap];0.85[AMR][1000 genomes]
rs10923006	0.92[ASN][1000 genomes]
rs10923008	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs12037980	0.81[ASN][1000 genomes]
rs172191	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1822056	1.00[CHB][hapmap];0.86[JPT][hapmap];0.82[AMR][1000 genomes]
rs281934	0.89[ASN][1000 genomes]
rs281953	0.93[ASN][1000 genomes]
rs281973	1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.99[ASN][1000 genomes]
rs281985	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs282000	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.97[LWK][hapmap];0.87[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs282003	0.81[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.83[LWK][hapmap];0.83[MEX][hapmap];0.93[MKK][hapmap];0.87[TSI][hapmap];0.91[YRI][hapmap];0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs282004	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.92[LWK][hapmap];0.87[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs282011	0.81[ASN][1000 genomes]
rs282017	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs282056	0.91[ASN][1000 genomes]
rs282057	1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs2893151	1.00[ASN][1000 genomes]
rs3893101	1.00[CHB][hapmap];0.95[JPT][hapmap];0.98[ASN][1000 genomes]
rs693299	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7541566	1.00[CHB][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs9660466	0.84[ASN][1000 genomes]
rs9663060	0.82[AMR][1000 genomes]
rs9728662	0.87[AMR][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	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs204304	HFM1	cis	cerebellum	SCAN
rs204304	HFM1	cis	parietal	SCAN

Chromatin state (count:23 , 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	chr1:91777000-91780400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr1:91777600-91781400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
9	chr1:91777600-91790600	Weak transcription	Fetal Brain Female	brain
10	chr1:91777600-91790600	Weak transcription	Skeletal Muscle Female	skeletal muscle
11	chr1:91777600-91790800	Weak transcription	Primary hematopoietic stem cells	blood
12	chr1:91777600-91794000	Weak transcription	Cortex derived primary cultured neurospheres	brain
13	chr1:91777800-91794600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr1:91778000-91790600	Weak transcription	Brain Germinal Matrix	brain
15	chr1:91778000-91790600	Weak transcription	Fetal Lung	lung
16	chr1:91778000-91793800	Weak transcription	Skeletal Muscle Male	skeletal muscle
17	chr1:91778000-91794000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr1:91778000-91794000	Weak transcription	Fetal Intestine Small	intestine
19	chr1:91778200-91782400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr1:91778600-91790400	Weak transcription	Fetal Stomach	stomach
21	chr1:91778600-91793800	Weak transcription	Ovary	ovary
22	chr1:91779000-91784400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr1:91779000-91793800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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