Variant report

Variant	rs982988
Chromosome Location	chr11:15897626-15897627
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 34 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10766289	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10766290	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10832526	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11023753	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11023757	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11023763	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11023766	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12270494	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12270765	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12287547	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12289250	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12290232	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12364139	0.93[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1440705	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1440707	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1866820	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2008923	0.84[AMR][1000 genomes]
rs2119376	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2218204	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2615023	0.84[AMR][1000 genomes]
rs2615024	0.84[AMR][1000 genomes]
rs4756835	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4756836	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4756837	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4757370	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4757371	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4757373	1.00[CEU][hapmap];0.88[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4757374	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4757375	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7106197	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7122245	0.83[AMR][1000 genomes]
rs7481566	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs965476	0.84[AMR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832073	chr11:15822409-15984078	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs982988	DKK3	cis	cerebellum	SCAN

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:15893600-15914000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr11:15894200-15897800	Weak transcription	HUES6 Cell Line	embryonic stem cell
3	chr11:15895400-15897800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr11:15895800-15900200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr11:15896000-15899400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr11:15897000-15898000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr11:15897000-15898000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr11:15897000-15898200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr11:15897000-15898200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr11:15897000-15898400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr11:15897000-15898400	Enhancers	HUES64 Cell Line	embryonic stem cell
12	chr11:15897000-15898400	Enhancers	Fetal Intestine Small	intestine
13	chr11:15897200-15898000	Enhancers	Cortex derived primary cultured neurospheres	brain
14	chr11:15897200-15898400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr11:15897400-15897800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr11:15897400-15898000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr11:15897400-15898000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
18	chr11:15897600-15898000	Enhancers	H9 Cell Line	embryonic stem cell
19	chr11:15897600-15898000	Enhancers	iPS-18 Cell Line	embryonic stem cell
20	chr11:15897600-15898200	Enhancers	Fetal Intestine Large	intestine

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