Variant report

Variant	rs550297
Chromosome Location	chr1:170115156-170115157
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 33 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10800501	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1411464	0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2786921	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4656205	0.90[ASN][1000 genomes]
rs471155	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs471569	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs471781	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs482571	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs493966	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs495125	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs495524	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs504942	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs514257	0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs522361	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs523222	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs524309	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs525285	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs532141	0.91[CHD][hapmap];0.89[GIH][hapmap];0.80[JPT][hapmap];0.87[MEX][hapmap];0.83[ASN][1000 genomes]
rs533387	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs548356	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs548582	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs551042	0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs556764	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs563559	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs572480	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs575119	0.80[ASW][hapmap];0.96[CEU][hapmap];0.90[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs576152	0.80[ASW][hapmap];0.96[CEU][hapmap];0.90[CHB][hapmap];0.82[CHD][hapmap];1.00[JPT][hapmap];0.98[TSI][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs579438	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6704499	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9427182	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[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	nsv1014033	chr1:169968488-170453021	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	18 gene(s)	inside rSNPs	diseases
2	nsv535200	chr1:169968488-170453021	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	18 gene(s)	inside rSNPs	diseases
3	nsv999310	chr1:170065943-170223350	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs550297	BLZF1	cis	cerebellum	SCAN
rs550297	BRP44	cis	parietal	SCAN

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:170114200-170115200	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
2	chr1:170114200-170115800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr1:170114200-170116200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr1:170114200-170116800	Enhancers	ES-I3 Cell Line	embryonic stem cell
5	chr1:170114200-170117000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr1:170114400-170115600	Enhancers	Fetal Brain Male	brain
7	chr1:170114600-170116800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr1:170114600-170117000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr1:170114800-170115200	Enhancers	Fetal Muscle Leg	muscle
10	chr1:170114800-170115200	Enhancers	Pancreas	Pancrea
11	chr1:170114800-170115400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr1:170114800-170115400	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr1:170114800-170115400	Active TSS	Right Ventricle	heart
14	chr1:170114800-170115600	Flanking Active TSS	Brain Germinal Matrix	brain
15	chr1:170114800-170116200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
16	chr1:170114800-170116200	Enhancers	Cortex derived primary cultured neurospheres	brain
17	chr1:170114800-170116400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr1:170114800-170116400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
19	chr1:170114800-170116800	Enhancers	Primary T cells from cord blood	blood
20	chr1:170115000-170115400	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
21	chr1:170115000-170115400	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell
22	chr1:170115000-170115400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr1:170115000-170115600	Enhancers	Fetal Brain Female	brain
24	chr1:170115000-170115800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
25	chr1:170115000-170115800	Active TSS	Fetal Heart	heart
26	chr1:170115000-170115800	Enhancers	Thymus	Thymus
27	chr1:170115000-170116000	Enhancers	HUES64 Cell Line	embryonic stem cell
28	chr1:170115000-170116200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr1:170115000-170116400	Active TSS	Right Atrium	heart
30	chr1:170115000-170116600	Enhancers	iPS-15b Cell Line	embryonic stem cell
31	chr1:170115000-170116600	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
32	chr1:170115000-170116800	Enhancers	HUES6 Cell Line	embryonic stem cell
33	chr1:170115000-170116800	Flanking Active TSS	Dnd41	blood

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