Variant report

Variant	rs10940291
Chromosome Location	chr5:52409259-52409260
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:0)
Chromatin interactive
region (count:3)
LncRNA
region (count:2)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:3 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOXA2	chr5:52408458-52409266	HepG2	liver:	n/a	n/a
2	CEBPZ	chr5:52409100-52409289	HepG2	liver:	n/a	n/a
3	FOXA1	chr5:52408570-52409261	HepG2	liver:	n/a	chr5:52408892-52408907

No data

(count:3 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr5:52385620..52387718-chr5:52408236..52410843,2	MCF-7	breast:
2	chr5:52402569..52404827-chr5:52408114..52410359,2	K562	blood:
3	chr5:52408413..52410275-chr5:52416214..52418011,2	K562	blood:

(count:2 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ITGA2-1	chr5:52408070-52409335	XLOC_004382
2	lnc-ITGA2-1	chr5:52408070-52410956	ENSG00000247796

No data

Variant related genes	Relation type
MOCS2	TF binding region
ENSG00000164172	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs10805445	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12515434	0.91[YRI][hapmap]
rs153601	0.86[JPT][hapmap]
rs17298242	0.89[CHB][hapmap];0.95[GIH][hapmap];0.86[ASN][1000 genomes]
rs17298431	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17298473	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.97[TSI][hapmap];0.92[YRI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1900182	0.84[ASN][1000 genomes]
rs2303124	0.86[ASN][1000 genomes]
rs62359377	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62359378	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949005	chr5:52188028-52808229	Flanking Bivalent TSS/Enh Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv830296	chr5:52209528-52410253	Strong transcription Enhancers Flanking Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
3	nsv442948	chr5:52404519-52409439	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs10940291	CTD-2366F13.1	cis	Stomach	GTEx
rs10940291	CTD-2366F13.1	cis	Artery Aorta	GTEx
rs10940291	CTD-2366F13.1	cis	Esophagus Muscularis	GTEx
rs10940291	AK097893	cis	multi-tissue	Pritchard

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:52406000-52414200	Weak transcription	Gastric	stomach
2	chr5:52406200-52410200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr5:52406200-52411400	Weak transcription	Aorta	Aorta
4	chr5:52406400-52411800	Weak transcription	Psoas Muscle	Psoas
5	chr5:52406400-52412400	Weak transcription	Ovary	ovary
6	chr5:52406400-52419000	Weak transcription	Left Ventricle	heart
7	chr5:52406600-52410400	Weak transcription	Thymus	Thymus
8	chr5:52406600-52414600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr5:52406800-52410000	Weak transcription	HUES48 Cell Line	embryonic stem cell
10	chr5:52406800-52410200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
11	chr5:52406800-52410600	Weak transcription	Primary hematopoietic stem cells	blood
12	chr5:52406800-52411600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr5:52406800-52414000	Weak transcription	Brain Hippocampus Middle	brain
14	chr5:52406800-52422000	Weak transcription	NHLF	lung
15	chr5:52406800-52422200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr5:52407000-52409800	Weak transcription	H1 Cell Line	embryonic stem cell
17	chr5:52407000-52410000	Weak transcription	Spleen	Spleen
18	chr5:52407000-52410200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
19	chr5:52407000-52410600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr5:52407000-52410600	Weak transcription	Dnd41	blood
21	chr5:52407000-52411800	Weak transcription	Brain Anterior Caudate	brain
22	chr5:52407000-52412200	Weak transcription	Primary T cells from cord blood	blood
23	chr5:52407000-52414800	Weak transcription	Pancreas	Pancrea
24	chr5:52407000-52418800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr5:52407000-52418800	Weak transcription	NHEK	skin
26	chr5:52407000-52419000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr5:52407200-52409800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr5:52407200-52410600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
29	chr5:52407200-52410600	Weak transcription	Brain Angular Gyrus	brain
30	chr5:52407200-52413400	Weak transcription	K562	blood
31	chr5:52407200-52418800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr5:52408400-52409400	Enhancers	Liver	Liver
33	chr5:52408400-52410200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
34	chr5:52408400-52410800	Enhancers	HepG2	liver
35	chr5:52408600-52414000	Weak transcription	Fetal Intestine Small	intestine

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