Variant report

Variant	rs11917733
Chromosome Location	chr3:60090683-60090684
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 35 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10510825	0.95[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.97[ASN][1000 genomes]
rs11130752	0.88[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs11130753	0.90[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs11130754	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.99[ASN][1000 genomes]
rs11919455	0.95[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs12636662	0.83[CHD][hapmap];0.94[JPT][hapmap];0.90[ASN][1000 genomes]
rs6764937	0.86[ASN][1000 genomes]
rs6772047	0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs6773849	0.87[JPT][hapmap];0.88[ASN][1000 genomes]
rs6807027	0.86[CHD][hapmap];0.88[JPT][hapmap];0.89[ASN][1000 genomes]
rs6807624	0.95[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs9871368	0.89[CHD][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs996174	0.86[CHD][hapmap];0.88[JPT][hapmap];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:22 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1014983	chr3:59884024-60558331	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv590387	chr3:59890976-60481459	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv834707	chr3:60005679-60184046	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	esv2752010	chr3:60067396-60288428	Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv1009063	chr3:60067866-60277128	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	nsv1013919	chr3:60067866-60284882	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	nsv519855	chr3:60068730-60276722	Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
8	nsv460566	chr3:60068730-60276722	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
9	nsv460567	chr3:60068730-60276722	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
10	nsv590390	chr3:60068730-60276722	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
11	nsv590391	chr3:60068730-60277709	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
12	nsv1008586	chr3:60070974-60258108	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
13	nsv536576	chr3:60070974-60258108	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
14	nsv1009971	chr3:60070974-60397331	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
15	nsv1008267	chr3:60071947-60264461	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
16	nsv1007798	chr3:60071947-60277128	Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
17	esv2763751	chr3:60071959-60292312	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
18	esv2752011	chr3:60073153-60288428	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
19	nsv432421	chr3:60073153-60288428	Weak transcription Enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
20	nsv876840	chr3:60083293-60194570	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
21	nsv529602	chr3:60088353-60830769	Enhancers Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
22	nsv915646	chr3:60088475-60240653	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11917733	EIF4B	cis	Frontal Cortex	GTEx
rs11917733	KCTD6	cis	cerebellum	SCAN

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:60086200-60091000	Enhancers	Fetal Intestine Large	intestine
2	chr3:60086200-60091600	Enhancers	Fetal Intestine Small	intestine
3	chr3:60088800-60090800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
4	chr3:60088800-60091200	Enhancers	Dnd41	blood
5	chr3:60088800-60091400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr3:60089400-60091000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr3:60089600-60090800	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr3:60089600-60091200	Enhancers	Primary T cells from cord blood	blood
9	chr3:60089600-60091800	Enhancers	Primary T helper cells PMA-I stimulated	--
10	chr3:60089600-60092000	Enhancers	Primary T helper cells fromperipheralblood	blood
11	chr3:60089800-60091400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr3:60089800-60091400	Enhancers	Cortex derived primary cultured neurospheres	brain
13	chr3:60089800-60091400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr3:60090000-60091200	Enhancers	Primary T helper naive cells from peripheral blood	blood
15	chr3:60090000-60091400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
16	chr3:60090200-60090800	Enhancers	Primary hematopoietic stem cells	blood
17	chr3:60090400-60090800	Enhancers	HUES64 Cell Line	embryonic stem cell
18	chr3:60090400-60091000	Enhancers	Brain Inferior Temporal Lobe	brain
19	chr3:60090400-60091000	Enhancers	Fetal Thymus	thymus
20	chr3:60090400-60091200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr3:60090400-60091200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
22	chr3:60090600-60091200	Enhancers	Brain Substantia Nigra	brain

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