Variant report

Variant	rs4780042
Chromosome Location	chr15:33129380-33129381
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RP11-632K20.1.1-3	chr15:33129184-33129527	NONHSAT041533

Extended variants
information (count: 15 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs12438573	1.00[CHB][hapmap]
rs1258797	1.00[CHB][hapmap]
rs12906786	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12916120	1.00[ASN][1000 genomes]
rs13329660	1.00[ASN][1000 genomes]
rs16963396	1.00[CHB][hapmap]
rs55752067	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62001277	1.00[ASN][1000 genomes]
rs7178265	1.00[CHB][hapmap];0.96[GIH][hapmap];0.86[MEX][hapmap];0.91[TSI][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2422296	chr15:32798938-33221215	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv456785	chr15:32926076-33352989	Genic enhancers Active TSS Weak transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv568913	chr15:32926076-33352989	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv482680	chr15:32958401-33154005	Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Genic enhancers Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv832961	chr15:33021177-33134988	Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv832962	chr15:33111517-33239736	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4780042	AVEN	cis	parietal	SCAN
rs4780042	GABRG3	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:33061200-33141000	Weak transcription	Placenta	Placenta
2	chr15:33096200-33154000	Weak transcription	Rectal Mucosa Donor 29	rectum
3	chr15:33096400-33159000	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr15:33103800-33139200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr15:33111200-33130000	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr15:33112000-33130600	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr15:33117800-33130800	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr15:33117800-33131000	Weak transcription	Stomach Smooth Muscle	stomach
9	chr15:33118600-33159000	Weak transcription	Gastric	stomach
10	chr15:33119400-33131600	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr15:33121800-33130600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr15:33122800-33130400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr15:33123000-33130800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr15:33124400-33130200	Weak transcription	A549	lung
15	chr15:33124600-33131200	Weak transcription	Lung	lung
16	chr15:33126000-33131200	Weak transcription	Stomach Mucosa	stomach
17	chr15:33126200-33130400	Weak transcription	NH-A	brain
18	chr15:33126200-33131000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr15:33126600-33129600	Weak transcription	NHDF-Ad	bronchial
20	chr15:33126800-33129600	Weak transcription	Muscle Satellite Cultured Cells	--
21	chr15:33126800-33130000	Weak transcription	Brain Angular Gyrus	brain
22	chr15:33126800-33130400	Weak transcription	HSMM	muscle
23	chr15:33127000-33130000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr15:33127000-33131000	Weak transcription	HSMMtube	muscle
25	chr15:33127000-33141400	Weak transcription	Monocytes-CD14+_RO01746	blood
26	chr15:33127200-33129800	Weak transcription	Pancreatic Islets	Pancreatic Islet
27	chr15:33127200-33131400	Weak transcription	HUES48 Cell Line	embryonic stem cell
28	chr15:33127400-33130000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr15:33127400-33130000	Weak transcription	NHLF	lung
30	chr15:33128000-33130800	Weak transcription	Duodenum Mucosa	Duodenum
31	chr15:33128400-33131400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
32	chr15:33128800-33130800	Weak transcription	Fetal Stomach	stomach
33	chr15:33129200-33129400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr15:33129200-33129600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr15:33129200-33129800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr15:33129200-33130000	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr15:33129200-33130000	Strong transcription	Osteobl	bone
38	chr15:33129200-33131600	Genic enhancers	Foreskin Melanocyte Primary Cells skin01	Skin

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