Variant report

Variant	rs60140893
Chromosome Location	chr3:49907911-49907912
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RFX5	chr3:49906091-49907927	SK-N-SH	brain:	n/a	chr3:49906789-49906804 chr3:49906789-49906804 chr3:49906789-49906804
2	MXI1	chr3:49906074-49907977	SK-N-SH	brain:	n/a	chr3:49906790-49906805 chr3:49906625-49906634 chr3:49906788-49906803 chr3:49906531-49906546

Variant related genes	Relation type
CAMKV	TF binding region

Extended variants
information (count: 11 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs35926013	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57466955	1.00[AMR][1000 genomes]
rs57654941	1.00[AMR][1000 genomes]
rs61669412	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61703429	1.00[AMR][1000 genomes]
rs6797308	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73834010	1.00[AMR][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	esv1796352	chr3:49687101-49949959	Genic enhancers Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
2	nsv834688	chr3:49811115-50019299	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
3	esv1809827	chr3:49812331-49934179	Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
4	nsv876766	chr3:49817450-49961780	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49906200-49908200	Active TSS	Brain Anterior Caudate	brain
2	chr3:49906600-49910800	Enhancers	Fetal Brain Male	brain
3	chr3:49907400-49908000	Flanking Active TSS	Brain Germinal Matrix	brain
4	chr3:49907400-49908200	Bivalent Enhancer	Brain Hippocampus Middle	brain
5	chr3:49907600-49908000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
6	chr3:49907600-49908000	Bivalent Enhancer	Duodenum Smooth Muscle	Duodenum
7	chr3:49907600-49908000	Flanking Active TSS	Fetal Brain Female	brain
8	chr3:49907600-49908200	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr3:49907600-49908600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr3:49907600-49909000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr3:49907600-49909400	Enhancers	Brain Angular Gyrus	brain
12	chr3:49907600-49909400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
13	chr3:49907600-49910800	Weak transcription	Gastric	stomach
14	chr3:49907800-49908000	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
15	chr3:49907800-49908000	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
16	chr3:49907800-49908000	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
17	chr3:49907800-49908000	Bivalent Enhancer	Fetal Intestine Large	intestine
18	chr3:49907800-49908000	Bivalent Enhancer	Dnd41	blood
19	chr3:49907800-49908400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr3:49907800-49908600	Bivalent Enhancer	Fetal Intestine Small	intestine
21	chr3:49907800-49908800	Weak transcription	Cortex derived primary cultured neurospheres	brain
22	chr3:49907800-49909600	Enhancers	Brain Inferior Temporal Lobe	brain
23	chr3:49907800-49911000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr3:49907800-49911200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived

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