Variant report

Variant	rs2491039
Chromosome Location	chr13:55210336-55210337
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 52 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs1020967	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1382461	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1471449	0.83[ASN][1000 genomes]
rs1600227	0.83[ASN][1000 genomes]
rs2185642	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2409105	0.87[EUR][1000 genomes]
rs2447970	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2491038	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2898093	0.86[EUR][1000 genomes]
rs55804851	0.82[ASN][1000 genomes]
rs55889672	0.97[ASN][1000 genomes]
rs55957980	0.93[ASN][1000 genomes]
rs56230005	0.88[EUR][1000 genomes]
rs56256911	0.97[ASN][1000 genomes]
rs61950895	0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7317305	0.83[ASN][1000 genomes]
rs7318471	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7323791	0.88[EUR][1000 genomes]
rs7326567	0.83[ASN][1000 genomes]
rs7328327	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7337743	0.87[EUR][1000 genomes]
rs7994187	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9316739	1.00[ASN][1000 genomes]
rs9527231	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9527237	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9527239	1.00[ASN][1000 genomes]
rs9527240	1.00[ASN][1000 genomes]
rs9527242	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9536767	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9536768	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9536769	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9536772	0.85[EUR][1000 genomes]
rs9536774	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9536775	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9536790	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9536792	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9536823	0.83[ASN][1000 genomes]
rs9536824	0.83[ASN][1000 genomes]
rs9536829	0.83[ASN][1000 genomes]
rs9536838	0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3349795	chr13:54892694-55252030	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv917186	chr13:55022134-55433232	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv561702	chr13:55086271-55808127	Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
4	nsv1043044	chr13:55102831-55285581	Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Weak transcription Active TSS	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv1048599	chr13:55143426-55476042	Flanking Active TSS Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv1051640	chr13:55143426-55478547	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
7	nsv561703	chr13:55143754-55473732	Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	nsv916104	chr13:55154006-55433232	Enhancers ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
9	nsv1052745	chr13:55159674-55459161	Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
10	nsv541779	chr13:55159674-55459161	Weak transcription Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
11	nsv1048372	chr13:55190941-55212421	Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
12	nsv1039752	chr13:55199645-55212421	Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2491039	ARL11	cis	parietal	SCAN
rs2491039	CKAP2	cis	cerebellum	SCAN

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:55207600-55210400	Weak transcription	HUES6 Cell Line	embryonic stem cell
2	chr13:55207800-55211400	Weak transcription	Cortex derived primary cultured neurospheres	brain
3	chr13:55208000-55210600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
4	chr13:55208000-55210600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
5	chr13:55208000-55211600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr13:55208000-55212600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr13:55208200-55211600	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr13:55210000-55210400	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr13:55210200-55210400	Enhancers	HUES64 Cell Line	embryonic stem cell
10	chr13:55210200-55210800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr13:55210200-55210800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr13:55210200-55210800	Enhancers	HUES48 Cell Line	embryonic stem cell
13	chr13:55210200-55210800	Enhancers	Fetal Intestine Small	intestine

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