Variant report

Variant	rs12153055
Chromosome Location	chr5:80300607-80300608
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 21 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs12152989	0.81[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs13156982	0.88[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs13157328	0.82[ASN][1000 genomes]
rs13176380	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs13177252	0.81[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs13179550	0.81[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs13182907	0.82[JPT][hapmap];0.90[YRI][hapmap];0.84[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs13183094	0.92[YRI][hapmap]
rs13183890	0.92[YRI][hapmap]
rs17409544	1.00[JPT][hapmap]
rs4704694	0.88[ASN][1000 genomes]
rs4704695	0.89[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.82[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs6879497	1.00[JPT][hapmap]
rs73766165	0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1024844	chr5:79862428-80860430	Weak transcription Strong transcription Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv598747	chr5:79996632-80322712	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv1021784	chr5:80023679-80313586	ZNF genes & repeats Bivalent Enhancer Strong transcription Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv537787	chr5:80023679-80313586	Weak transcription Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
5	nsv830358	chr5:80197105-80358920	Flanking Bivalent TSS/Enh Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	nsv830360	chr5:80283278-80446040	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	nsv4897	chr5:80284196-80330223	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12153055	RASGRF2	cis	parietal	SCAN

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:80291400-80302400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
2	chr5:80294800-80302400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr5:80298400-80302200	Enhancers	Primary T helper cells fromperipheralblood	blood
4	chr5:80299400-80302200	Enhancers	Primary T cells fromperipheralblood	blood
5	chr5:80299400-80302400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
6	chr5:80299600-80300800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
7	chr5:80299600-80302200	Enhancers	Primary T helper naive cells from peripheral blood	blood
8	chr5:80299600-80302400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
9	chr5:80299600-80302400	Enhancers	Primary T killer memory cells from peripheral blood	blood
10	chr5:80299600-80304400	Enhancers	Fetal Thymus	thymus
11	chr5:80299800-80300800	Enhancers	Fetal Lung	lung
12	chr5:80299800-80301000	Enhancers	Brain Cingulate Gyrus	brain
13	chr5:80300000-80313000	Weak transcription	Cortex derived primary cultured neurospheres	brain
14	chr5:80300200-80301200	Enhancers	Adipose Nuclei	Adipose
15	chr5:80300200-80302000	Weak transcription	Dnd41	blood
16	chr5:80300200-80302200	Weak transcription	HepG2	liver
17	chr5:80300200-80302400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr5:80300400-80300800	Weak transcription	Left Ventricle	heart
19	chr5:80300400-80301600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr5:80300400-80302200	Enhancers	Primary T helper cells PMA-I stimulated	--
21	chr5:80300400-80302200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr5:80300400-80302400	Weak transcription	Right Atrium	heart
23	chr5:80300400-80302800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr5:80300400-80304800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr5:80300400-80312800	Weak transcription	Brain Hippocampus Middle	brain
26	chr5:80300400-80316600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr5:80300400-80318400	Weak transcription	Brain Inferior Temporal Lobe	brain
28	chr5:80300600-80301000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
29	chr5:80300600-80302000	Enhancers	Primary T cells from cord blood	blood
30	chr5:80300600-80302000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
31	chr5:80300600-80302000	Weak transcription	Thymus	Thymus
32	chr5:80300600-80302600	Weak transcription	Brain Angular Gyrus	brain
33	chr5:80300600-80303400	Weak transcription	Brain Substantia Nigra	brain

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