Variant report

Variant	rs920469
Chromosome Location	chr1:91789353-91789354
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 46 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs12408911	0.83[AMR][1000 genomes]
rs12562039	0.96[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs12562097	0.85[AMR][1000 genomes]
rs12564415	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12566911	0.85[AMR][1000 genomes]
rs12567679	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.93[GIH][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.95[TSI][hapmap];0.85[AMR][1000 genomes]
rs12567930	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];1.00[LWK][hapmap];0.93[MEX][hapmap];0.98[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12729858	1.00[CEU][hapmap];0.81[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12746156	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12749858	0.87[AMR][1000 genomes]
rs12756869	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];0.93[JPT][hapmap];1.00[LWK][hapmap];0.93[MEX][hapmap];0.98[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs12757442	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12759453	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12760267	0.91[CEU][hapmap];0.85[CHB][hapmap];0.89[CHD][hapmap];0.98[GIH][hapmap];0.93[JPT][hapmap];0.93[MEX][hapmap];0.86[MKK][hapmap];0.97[TSI][hapmap]
rs1610018	0.87[AMR][1000 genomes]
rs17131418	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];0.93[JPT][hapmap];1.00[LWK][hapmap];0.93[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1822057	0.87[AMR][1000 genomes]
rs1974253	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2060997	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2099749	0.80[CEU][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28395174	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34105527	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34507721	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34600283	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34744207	0.85[AMR][1000 genomes]
rs34760954	0.82[AMR][1000 genomes]
rs34809593	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34840774	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34999283	0.87[AMR][1000 genomes]
rs35081855	0.92[AMR][1000 genomes]
rs35462750	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4248874	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes]
rs4658206	0.87[AMR][1000 genomes]
rs4658210	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4658215	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs58986615	0.83[AMR][1000 genomes]
rs60685596	0.83[AMR][1000 genomes]
rs66715895	0.87[AMR][1000 genomes]
rs66730201	0.94[AMR][1000 genomes]
rs67955041	0.87[AMR][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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs920469	HFM1	cis	cerebellum	SCAN
rs920469	ABCA4	cis	parietal	SCAN
rs920469	HFM1	cis	parietal	SCAN
rs920469	CCDC18	cis	parietal	SCAN

Chromatin state (count:27 , 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	chr1:91778600-91790400	Weak transcription	Fetal Stomach	stomach
18	chr1:91778600-91793800	Weak transcription	Ovary	ovary
19	chr1:91779000-91793800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr1:91782600-91804800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr1:91786200-91795000	Weak transcription	Psoas Muscle	Psoas
22	chr1:91786800-91790600	Weak transcription	Fetal Muscle Trunk	muscle
23	chr1:91788200-91793800	Weak transcription	Stomach Smooth Muscle	stomach
24	chr1:91788400-91810800	Weak transcription	Brain Cingulate Gyrus	brain
25	chr1:91788800-91790600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr1:91788800-91795800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr1:91789000-91794000	Weak transcription	Pancreatic Islets	Pancreatic Islet

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