Variant report

Variant	rs7544677
Chromosome Location	chr1:170131767-170131768
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:170129471..170132945-chr1:170134793..170138535,3	K562	blood:

Extended variants
information (count: 38 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10800498	0.87[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs10800500	1.00[CHB][hapmap];0.94[CHD][hapmap];0.92[JPT][hapmap];0.86[LWK][hapmap];0.82[MEX][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs10800502	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10800505	0.81[ASN][1000 genomes]
rs10800506	0.81[ASN][1000 genomes]
rs10919306	1.00[CHB][hapmap];0.92[JPT][hapmap];0.93[YRI][hapmap];0.90[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs10919307	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];0.92[JPT][hapmap];0.93[LWK][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10919309	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10919312	0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10919321	0.81[ASN][1000 genomes]
rs10919322	0.81[ASN][1000 genomes]
rs10919324	0.81[ASN][1000 genomes]
rs11484822	0.81[ASN][1000 genomes]
rs11484824	0.81[ASN][1000 genomes]
rs12039113	0.81[ASN][1000 genomes]
rs12569092	0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12751063	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2901341	0.81[ASN][1000 genomes]
rs35081369	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4332407	1.00[CHB][hapmap];0.92[JPT][hapmap];0.93[YRI][hapmap];0.91[AFR][1000 genomes];0.80[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs477960	0.87[AFR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs480667	0.88[AFR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs490771	0.87[ASN][1000 genomes]
rs495127	0.81[CHB][hapmap];0.85[JPT][hapmap]
rs519459	0.81[CHB][hapmap];0.85[JPT][hapmap]
rs533666	0.81[ASN][1000 genomes]
rs550575	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs561326	0.81[CHB][hapmap];0.85[JPT][hapmap];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs562931	0.81[CHB][hapmap];0.85[JPT][hapmap];0.93[YRI][hapmap];0.87[AFR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs569357	0.81[ASN][1000 genomes]
rs6427234	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6427235	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6427236	0.85[JPT][hapmap]
rs6669514	0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs979347	0.87[AFR][1000 genomes];0.90[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7544677	MGST3	cis	cerebellum	SCAN

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:170126200-170135600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr1:170131000-170132000	Weak transcription	Right Ventricle	heart
3	chr1:170131200-170131800	Weak transcription	Fetal Muscle Trunk	muscle
4	chr1:170131200-170132000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr1:170131200-170133000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr1:170131400-170132200	Enhancers	Fetal Muscle Leg	muscle
7	chr1:170131400-170132400	Enhancers	Psoas Muscle	Psoas
8	chr1:170131400-170132400	Enhancers	Skeletal Muscle Male	skeletal muscle
9	chr1:170131400-170132400	Enhancers	Skeletal Muscle Female	skeletal muscle
10	chr1:170131400-170132600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr1:170131400-170132600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr1:170131400-170132600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr1:170131400-170132600	Enhancers	Breast Myoepithelial Primary Cells	Breast
14	chr1:170131400-170132600	Enhancers	HSMM	muscle
15	chr1:170131400-170132600	Enhancers	NH-A	brain
16	chr1:170131400-170132600	Enhancers	Osteobl	bone
17	chr1:170131400-170133200	Enhancers	NHDF-Ad	bronchial
18	chr1:170131600-170131800	Flanking Active TSS	Fetal Heart	heart
19	chr1:170131600-170131800	Flanking Active TSS	HSMMtube	muscle
20	chr1:170131600-170132200	Weak transcription	Left Ventricle	heart
21	chr1:170131600-170132600	Enhancers	Muscle Satellite Cultured Cells	--
22	chr1:170131600-170132600	Enhancers	NHLF	lung
23	chr1:170131600-170132800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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