Variant report

Variant	rs6677504
Chromosome Location	chr1:56786354-56786355
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 15 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs12030284	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12030407	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12043349	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12138574	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4912176	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs57354037	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs57578827	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs60984146	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs61772691	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61772727	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs61772729	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7555594	0.84[AMR][1000 genomes];0.98[EUR][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	nsv1006422	chr1:56734772-56828606	Flanking Active TSS Weak transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
2	nsv534972	chr1:56734772-56828606	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
3	nsv1015037	chr1:56784322-56814739	Enhancers Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6677504	TMEM59	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:56765200-56795400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr1:56768200-56791000	Weak transcription	Aorta	Aorta
3	chr1:56769600-56788000	Weak transcription	Right Atrium	heart
4	chr1:56770000-56791200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr1:56770400-56792200	Weak transcription	Right Ventricle	heart
6	chr1:56770600-56786600	Weak transcription	Left Ventricle	heart
7	chr1:56780200-56786600	Weak transcription	Psoas Muscle	Psoas
8	chr1:56780400-56793600	Weak transcription	Liver	Liver
9	chr1:56781800-56791000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr1:56782000-56797000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr1:56784200-56788000	Enhancers	NHDF-Ad	bronchial
12	chr1:56784200-56791000	Weak transcription	Ovary	ovary
13	chr1:56784200-56792200	Weak transcription	Lung	lung
14	chr1:56785600-56787000	Enhancers	Fetal Lung	lung
15	chr1:56785600-56787200	Enhancers	Fetal Muscle Leg	muscle
16	chr1:56785600-56787400	Enhancers	Fetal Heart	heart
17	chr1:56785800-56787000	Enhancers	Stomach Smooth Muscle	stomach
18	chr1:56786000-56786600	Enhancers	Adipose Nuclei	Adipose
19	chr1:56786000-56787000	Enhancers	Skeletal Muscle Female	skeletal muscle
20	chr1:56786200-56786800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr1:56786200-56787000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
22	chr1:56786200-56787000	Enhancers	Fetal Stomach	stomach
23	chr1:56786200-56787000	Enhancers	Skeletal Muscle Male	skeletal muscle

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