Variant report

Variant	rs6049757
Chromosome Location	chr20:24508421-24508422
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 26 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs13041310	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1555892	0.87[ASW][hapmap];0.89[CEU][hapmap];0.94[CHD][hapmap];0.92[GIH][hapmap];0.88[LWK][hapmap];0.95[MEX][hapmap];0.83[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2386954	0.80[CEU][hapmap];0.94[CHD][hapmap];0.92[GIH][hapmap];0.91[MEX][hapmap];0.80[TSI][hapmap];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2386956	1.00[CEU][hapmap];0.85[GIH][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4283490	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6036832	0.89[CEU][hapmap];1.00[LWK][hapmap];0.82[MEX][hapmap];0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6049755	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6049758	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6049759	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6049760	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6049765	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6049768	1.00[CEU][hapmap];0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6049771	0.89[CEU][hapmap];1.00[LWK][hapmap];0.82[MEX][hapmap];0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6049775	1.00[CEU][hapmap];1.00[LWK][hapmap];0.86[MEX][hapmap];0.83[TSI][hapmap];0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6076233	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6076235	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6114752	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6114757	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6114760	0.82[CHD][hapmap];0.88[EUR][1000 genomes]
rs6114768	0.85[CEU][hapmap];0.88[LWK][hapmap];0.82[EUR][1000 genomes]
rs6132738	0.82[CHD][hapmap]
rs6132742	0.87[ASW][hapmap];0.89[CEU][hapmap];1.00[LWK][hapmap];0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6132743	0.89[CEU][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6138316	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]

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	nsv9793	chr20:23939613-24734850	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv1058146	chr20:24210196-24531087	Bivalent Enhancer Weak transcription Flanking Active TSS Bivalent/Poised TSS Enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6049757	CST9	cis	parietal	SCAN
rs6049757	CST5	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:24491400-24508600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr20:24503400-24511000	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr20:24503800-24511200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr20:24504000-24525800	Weak transcription	Aorta	Aorta
5	chr20:24505000-24509200	Weak transcription	Brain Hippocampus Middle	brain
6	chr20:24505000-24509800	Weak transcription	Brain Anterior Caudate	brain
7	chr20:24505000-24509800	Weak transcription	Brain Cingulate Gyrus	brain
8	chr20:24505000-24510800	Weak transcription	Brain Germinal Matrix	brain
9	chr20:24505600-24509200	Weak transcription	Brain Substantia Nigra	brain
10	chr20:24505600-24509400	Weak transcription	Brain Angular Gyrus	brain
11	chr20:24505600-24509600	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr20:24506800-24510400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr20:24507800-24508600	Enhancers	iPS-18 Cell Line	embryonic stem cell
14	chr20:24508200-24509400	Enhancers	H1 Cell Line	embryonic stem cell
15	chr20:24508200-24523800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr20:24508400-24508600	Enhancers	Fetal Brain Male	brain

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