Variant report

Variant	rs41381544
Chromosome Location	chr3:54739411-54739412
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:54738031..54740045-chr3:54741949..54744426,2	K562	blood:

Extended variants
information (count: 57 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10510769	1.00[ASN][1000 genomes]
rs10510770	1.00[ASN][1000 genomes]
rs10510772	0.81[CEU][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1130197	1.00[ASN][1000 genomes]
rs11914640	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11914780	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11918101	0.86[AMR][1000 genomes]
rs11924275	1.00[YRI][hapmap];0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11925949	0.82[GIH][hapmap]
rs12185982	1.00[YRI][hapmap];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1427774	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17054227	1.00[ASN][1000 genomes]
rs17054246	1.00[ASW][hapmap];0.93[LWK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17054250	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[LWK][hapmap];0.86[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17054340	0.96[TSI][hapmap];0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17815617	1.00[ASN][1000 genomes]
rs17816548	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17816566	0.87[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1863858	0.89[ASW][hapmap];0.88[MEX][hapmap];0.83[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs28455661	0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2884808	1.00[ASN][1000 genomes]
rs34478567	0.89[ASW][hapmap];0.81[CEU][hapmap];1.00[LWK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4345041	1.00[ASN][1000 genomes]
rs4386460	1.00[ASN][1000 genomes]
rs55675480	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55772258	1.00[ASN][1000 genomes]
rs56008232	1.00[ASN][1000 genomes]
rs56112781	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56209938	1.00[ASN][1000 genomes]
rs56976748	1.00[ASN][1000 genomes]
rs57924227	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs58295654	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59004379	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62255527	1.00[ASN][1000 genomes]
rs62255533	1.00[ASN][1000 genomes]
rs62255534	1.00[ASN][1000 genomes]
rs62255535	1.00[ASN][1000 genomes]
rs62255536	1.00[ASN][1000 genomes]
rs62255538	1.00[ASN][1000 genomes]
rs6803005	1.00[ASN][1000 genomes]
rs72870661	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72870676	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72870688	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72872218	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72872226	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72872229	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72872244	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72872259	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72872285	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs72872300	0.83[AMR][1000 genomes]
rs72874203	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs72874204	0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73068445	1.00[ASN][1000 genomes]
rs7624695	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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs41381544	DNAH12	cis	cerebellum	SCAN
rs41381544	ESRG	cis	Whole Blood	GTEx
rs41381544	C3orf78	cis	cerebellum	SCAN

Chromatin state (count:22 , 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	chr3:54737000-54740600	Enhancers	HUES48 Cell Line	embryonic stem cell
3	chr3:54737200-54740200	Enhancers	HUES64 Cell Line	embryonic stem cell
4	chr3:54737400-54739600	Enhancers	iPS-20b Cell Line	embryonic stem cell
5	chr3:54737400-54739800	Enhancers	iPS-18 Cell Line	embryonic stem cell
6	chr3:54737600-54739600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
7	chr3:54737600-54739600	Enhancers	Cortex derived primary cultured neurospheres	brain
8	chr3:54737600-54742200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr3:54737800-54739800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr3:54737800-54741800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr3:54738000-54739800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr3:54738000-54740000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr3:54738000-54742400	Weak transcription	H1 Cell Line	embryonic stem cell
14	chr3:54738000-54743400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr3:54738200-54743600	Weak transcription	HUES6 Cell Line	embryonic stem cell
16	chr3:54738400-54741600	Enhancers	Fetal Muscle Leg	muscle
17	chr3:54738600-54741800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
18	chr3:54738800-54739600	Enhancers	Ovary	ovary
19	chr3:54738800-54739800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr3:54739000-54741600	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr3:54739200-54739600	Enhancers	ES-WA7 Cell Line	embryonic stem cell
22	chr3:54739200-54740200	Enhancers	ES-I3 Cell Line	embryonic stem cell

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