Variant report

Variant	rs16880892
Chromosome Location	chr5:52409245-52409246
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: 66 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs10044163	0.81[CEU][hapmap]
rs10045657	0.82[CEU][hapmap]
rs10055919	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10072821	0.82[CEU][hapmap]
rs10471372	0.81[CEU][hapmap]
rs10471829	0.89[CEU][hapmap]
rs10471830	0.89[CEU][hapmap]
rs10471831	0.82[CEU][hapmap]
rs10471832	0.82[CEU][hapmap]
rs1139484	0.83[AMR][1000 genomes]
rs13356629	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1445940	0.89[CEU][hapmap]
rs16880872	0.89[CEU][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs16880873	0.89[CEU][hapmap]
rs16880890	0.81[CEU][hapmap]
rs16880902	0.81[CEU][hapmap]
rs2052567	0.82[CEU][hapmap]
rs2233214	0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2303125	1.00[ASN][1000 genomes]
rs28413530	0.89[ASN][1000 genomes]
rs28841614	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2910966	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2974984	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3021373	0.83[AMR][1000 genomes]
rs3212327	0.89[CEU][hapmap]
rs3212429	0.89[ASN][1000 genomes]
rs3212444	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3212468	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3212487	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3212491	0.83[AMR][1000 genomes]
rs3212492	0.83[AMR][1000 genomes]
rs3212493	0.83[AMR][1000 genomes]
rs3212497	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3212498	0.83[AMR][1000 genomes]
rs3212503	0.83[AMR][1000 genomes]
rs3212504	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3212515	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3212523	0.89[CEU][hapmap];0.83[AMR][1000 genomes]
rs3212526	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3212528	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3212529	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3212543	0.83[AMR][1000 genomes]
rs3212544	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3212545	0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs3212558	1.00[ASN][1000 genomes]
rs3212570	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3212579	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3212583	0.88[CEU][hapmap]
rs3212585	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3212588	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3212593	1.00[ASN][1000 genomes]
rs3212607	1.00[ASN][1000 genomes]
rs3212613	1.00[ASN][1000 genomes]
rs3212615	1.00[ASN][1000 genomes]
rs3212629	0.89[CEU][hapmap]
rs3212630	0.89[CEU][hapmap]
rs3213805	0.89[CEU][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs3797468	0.80[CEU][hapmap]
rs3797469	0.80[CEU][hapmap]
rs7446448	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7737412	0.89[CEU][hapmap]
rs875657	0.89[CEU][hapmap]
rs9292009	0.82[CEU][hapmap]

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

No data

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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