Variant report

Variant	rs11925949
Chromosome Location	chr3:54728042-54728043
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 44 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10510771	1.00[ASW][hapmap];0.86[CEU][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.91[MEX][hapmap];0.86[MKK][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10510772	1.00[JPT][hapmap];0.87[LWK][hapmap]
rs1130197	1.00[JPT][hapmap]
rs11914780	1.00[JPT][hapmap]
rs11914973	0.80[CEU][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11920788	0.80[CEU][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11924275	1.00[JPT][hapmap]
rs12185982	1.00[JPT][hapmap]
rs17054227	1.00[JPT][hapmap]
rs17054246	1.00[JPT][hapmap]
rs17054250	1.00[JPT][hapmap]
rs17054291	1.00[ASW][hapmap];0.86[CEU][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.91[MEX][hapmap];0.98[MKK][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17054293	1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17054295	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17054340	1.00[JPT][hapmap];0.87[LWK][hapmap]
rs17815617	1.00[JPT][hapmap]
rs17816548	1.00[JPT][hapmap]
rs17816566	0.82[GIH][hapmap]
rs1863858	1.00[JPT][hapmap]
rs2359857	1.00[JPT][hapmap]
rs2884808	1.00[JPT][hapmap]
rs34478567	1.00[JPT][hapmap]
rs34590038	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41381544	0.82[GIH][hapmap]
rs4345041	1.00[JPT][hapmap]
rs4358270	1.00[JPT][hapmap]
rs4386460	1.00[JPT][hapmap]
rs55962540	0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56063440	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs566884	0.82[CEU][hapmap]
rs59796966	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60303224	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61267487	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66795104	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67730102	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6784130	0.86[YRI][hapmap];0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6803005	1.00[JPT][hapmap]
rs72870690	0.88[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs737517	1.00[JPT][hapmap];0.82[YRI][hapmap];0.85[AFR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7624695	1.00[JPT][hapmap]
rs7641640	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[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	nsv1014595	chr3:53944473-54846754	Enhancers Bivalent Enhancer Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv428084	chr3:54404258-54742756	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv834700	chr3:54637374-54803896	Weak transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11925949	DNAH12	cis	cerebellum	SCAN
rs11925949	STAB1	cis	cerebellum	SCAN

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:54713600-54743400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr3:54725600-54730200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr3:54725600-54731200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr3:54725800-54728200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr3:54725800-54728400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr3:54725800-54729800	Weak transcription	HMEC	breast
7	chr3:54725800-54730000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr3:54725800-54730000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr3:54725800-54730200	Weak transcription	HUES6 Cell Line	embryonic stem cell
10	chr3:54725800-54730400	Weak transcription	HUES48 Cell Line	embryonic stem cell
11	chr3:54725800-54731600	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr3:54725800-54731600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
13	chr3:54726000-54730200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr3:54726000-54731400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
15	chr3:54726600-54730400	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr3:54726600-54731400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr3:54726800-54728400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr3:54726800-54731400	Weak transcription	HUES64 Cell Line	embryonic stem cell

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