Variant report

Variant	rs2576203
Chromosome Location	chr1:217073060-217073061
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 13 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs1030849	0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11117718	0.81[ASN][1000 genomes]
rs11117720	1.00[CHB][hapmap];0.86[GIH][hapmap];0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs12563547	1.00[ASN][1000 genomes]
rs1436880	1.00[CHB][hapmap];0.82[ASN][1000 genomes]
rs1898312	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2576205	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.83[YRI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2576206	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.83[YRI][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3795704	1.00[CHB][hapmap];0.86[GIH][hapmap]
rs61325680	1.00[ASN][1000 genomes]
rs956977	0.87[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv873179	chr1:217056893-217112871	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
2	nsv873180	chr1:217073060-217112871	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2576203	ATF3	cis	cerebellum	SCAN
rs2576203	SLC30A1	cis	parietal	SCAN

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:217062600-217078000	Weak transcription	Pancreas	Pancrea
2	chr1:217062800-217076000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr1:217062800-217076200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr1:217062800-217087800	Weak transcription	Fetal Muscle Leg	muscle
5	chr1:217067400-217075800	Weak transcription	Fetal Intestine Large	intestine
6	chr1:217067800-217076000	Weak transcription	Skeletal Muscle Female	skeletal muscle
7	chr1:217068200-217076000	Weak transcription	Left Ventricle	heart
8	chr1:217071400-217073400	Enhancers	NHEK	skin
9	chr1:217072000-217073200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr1:217072000-217073200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr1:217072000-217073200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr1:217072000-217073200	Enhancers	HMEC	breast
13	chr1:217072200-217082800	Enhancers	Breast Myoepithelial Primary Cells	Breast
14	chr1:217072600-217074200	Weak transcription	Fetal Intestine Small	intestine
15	chr1:217073000-217073200	Enhancers	Brain Angular Gyrus	brain
16	chr1:217073000-217074000	Enhancers	Fetal Lung	lung

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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