Variant report

Variant	rs17799799
Chromosome Location	chr4:56968671-56968672
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 31 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10004059	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10010411	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10033958	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13101795	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13101982	0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13118922	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13119109	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13120985	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13121962	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13138694	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1531585	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17086308	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17086320	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17743434	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs28488125	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs34048981	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs34552342	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs35352417	0.98[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs35623860	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4865051	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4865052	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4865053	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4865054	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs71601619	0.96[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	esv2755990	chr4:56317136-57143037	Strong transcription Weak transcription Flanking Bivalent TSS/Enh Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
2	nsv1005845	chr4:56522075-56980357	Active TSS Bivalent Enhancer Weak transcription Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
3	nsv999328	chr4:56942917-57041586	Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
4	nsv1007114	chr4:56942917-57055381	Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
5	nsv999639	chr4:56942917-57401310	Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
6	nsv1014045	chr4:56942917-57404511	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
7	nsv1012036	chr4:56963544-57106642	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17799799	LRRC66	cis	parietal	SCAN

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:56948800-56972200	Weak transcription	Fetal Stomach	stomach
2	chr4:56952000-57024400	Weak transcription	Fetal Intestine Small	intestine
3	chr4:56952800-56978200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr4:56957600-56971800	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr4:56963800-56974600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr4:56964400-56969400	Enhancers	Cortex derived primary cultured neurospheres	brain
7	chr4:56965800-56974000	Weak transcription	Primary hematopoietic stem cells	blood
8	chr4:56966000-56971600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr4:56966000-56973200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr4:56966000-56973800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr4:56966000-56981200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
12	chr4:56967400-56979400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr4:56967800-56969400	Enhancers	Fetal Brain Female	brain
14	chr4:56968200-56968800	Enhancers	Fetal Kidney	kidney
15	chr4:56968200-56969200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr4:56968200-56969200	Enhancers	Fetal Brain Male	brain
17	chr4:56968200-56969600	Enhancers	Brain Germinal Matrix	brain
18	chr4:56968400-56969000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr4:56968400-56969200	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr4:56968600-56969200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr4:56968600-56969200	Enhancers	Fetal Heart	heart

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