Variant report

Variant	rs7110052
Chromosome Location	chr11:57104492-57104493
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 35 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10792086	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.90[MEX][hapmap];0.86[TSI][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10792088	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10792089	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10792091	0.92[ASN][1000 genomes]
rs10896598	0.92[ASN][1000 genomes]
rs10896603	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10896604	1.00[CHD][hapmap];0.92[ASN][1000 genomes]
rs10896605	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[MEX][hapmap];0.93[TSI][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10896608	1.00[CHD][hapmap];0.92[ASN][1000 genomes]
rs11228995	0.92[ASN][1000 genomes]
rs11228997	1.00[CHD][hapmap];0.92[ASN][1000 genomes]
rs11229003	0.92[ASN][1000 genomes]
rs11229011	0.92[ASN][1000 genomes]
rs11602265	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11602266	0.92[ASN][1000 genomes]
rs11603691	0.92[ASN][1000 genomes]
rs11607950	0.92[ASN][1000 genomes]
rs12365472	0.92[ASN][1000 genomes]
rs12576878	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1815769	0.92[ASN][1000 genomes]
rs2230649	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34135716	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4938863	1.00[CHD][hapmap];0.84[ASN][1000 genomes]
rs4938864	0.92[ASN][1000 genomes]
rs61888886	0.92[ASN][1000 genomes]
rs61888887	0.92[ASN][1000 genomes]
rs61888888	0.92[ASN][1000 genomes]
rs7106462	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7111339	0.92[ASN][1000 genomes]
rs7129491	1.00[CHD][hapmap];0.92[ASN][1000 genomes]
rs7951793	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.90[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv915640	chr11:56814841-57139786	Weak transcription Transcr. at gene 5' and 3' Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	nsv1044030	chr11:57073395-58035564	Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
3	nsv541047	chr11:57073395-58035564	Active TSS Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
4	nsv541048	chr11:57076815-57120781	Flanking Active TSS Genic enhancers Active TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7110052	PRPF19	cis	cerebellum	SCAN
rs7110052	OR8I2	cis	cerebellum	SCAN
rs7110052	TIMM10	cis	parietal	SCAN

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:57103800-57105400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr11:57103800-57110000	Weak transcription	Fetal Brain Female	brain
3	chr11:57104000-57104600	Enhancers	Primary T cells fromperipheralblood	blood
4	chr11:57104000-57104600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
5	chr11:57104000-57105400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr11:57104000-57105400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr11:57104000-57105400	Weak transcription	HUES6 Cell Line	embryonic stem cell
8	chr11:57104000-57105400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr11:57104000-57105800	Weak transcription	Left Ventricle	heart
10	chr11:57104000-57106000	Weak transcription	H1 Cell Line	embryonic stem cell
11	chr11:57104000-57106400	Weak transcription	HUES64 Cell Line	embryonic stem cell
12	chr11:57104000-57106800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr11:57104000-57106800	Weak transcription	Fetal Brain Male	brain
14	chr11:57104000-57107200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr11:57104000-57113000	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr11:57104000-57117200	Weak transcription	Right Atrium	heart
17	chr11:57104200-57105400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr11:57104200-57105400	Weak transcription	Fetal Muscle Trunk	muscle
19	chr11:57104200-57105400	Weak transcription	Fetal Muscle Leg	muscle
20	chr11:57104200-57105400	Weak transcription	Fetal Stomach	stomach
21	chr11:57104200-57105600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr11:57104200-57117000	Weak transcription	Adipose Nuclei	Adipose
23	chr11:57104200-57117000	Weak transcription	Liver	Liver
24	chr11:57104200-57119200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr11:57104400-57104600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
26	chr11:57104400-57104600	Enhancers	Primary T helper cells PMA-I stimulated	--
27	chr11:57104400-57104600	Enhancers	Dnd41	blood
28	chr11:57104400-57105400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr11:57104400-57105400	Weak transcription	Fetal Lung	lung
30	chr11:57104400-57105600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr11:57104400-57106600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr11:57104400-57107000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr11:57104400-57107000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
34	chr11:57104400-57107200	Weak transcription	Fetal Thymus	thymus
35	chr11:57104400-57107400	Weak transcription	K562	blood
36	chr11:57104400-57107600	Weak transcription	A549	lung
37	chr11:57104400-57109000	Weak transcription	GM12878-XiMat	blood
38	chr11:57104400-57111000	Weak transcription	Primary hematopoietic stem cells short term culture	blood

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