Variant report

Variant	rs10471372
Chromosome Location	chr5:52408132-52408133
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CBX3	chr5:52408045-52408607	K562	blood:	n/a	n/a
2	NFYB	chr5:52408052-52408586	K562	blood:	n/a	chr5:52408308-52408323 chr5:52408332-52408347 chr5:52408356-52408371
3	NFYA	chr5:52407914-52408584	K562	blood:	n/a	chr5:52408359-52408377

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:52402569..52404827-chr5:52408114..52410359,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ITGA2-1	chr5:52408070-52409335	XLOC_004382
2	lnc-ITGA2-1	chr5:52408070-52408396	XLOC_004382
3	lnc-ITGA2-1	chr5:52408070-52410956	ENSG00000247796
4	lnc-ITGA2-1	chr5:52408070-52408864	ENSG00000247796
5	lnc-ITGA2-1	chr5:52408070-52408864	NR_034107
6	lnc-ITGA2-1	chr5:52408070-52408864	XLOC_004382

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

Extended variants
information (count: 29 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10044163	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10045657	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10052267	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10064796	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10072821	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10471831	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10471832	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16880890	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16880892	0.81[CEU][hapmap]
rs16880902	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2052567	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2062562	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2233213	0.85[CHB][hapmap];0.86[CHD][hapmap]
rs2233216	0.86[CHB][hapmap];0.86[CHD][hapmap]
rs28841614	0.91[AFR][1000 genomes]
rs28861745	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28890193	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3212437	0.86[CHB][hapmap]
rs3797468	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3797469	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3816326	0.86[CHB][hapmap];0.86[CHD][hapmap]
rs3846488	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4555727	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7446448	0.80[CEU][hapmap]
rs9292008	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9292009	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10471372	LAYN	trans	cerebellum	SCAN

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	chr5:52406800-52408200	Weak transcription	Fetal Intestine Small	intestine
10	chr5:52406800-52410000	Weak transcription	HUES48 Cell Line	embryonic stem cell
11	chr5:52406800-52410200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
12	chr5:52406800-52410600	Weak transcription	Primary hematopoietic stem cells	blood
13	chr5:52406800-52411600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr5:52406800-52414000	Weak transcription	Brain Hippocampus Middle	brain
15	chr5:52406800-52422000	Weak transcription	NHLF	lung
16	chr5:52406800-52422200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr5:52407000-52408200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr5:52407000-52408400	Weak transcription	Liver	Liver
19	chr5:52407000-52409800	Weak transcription	H1 Cell Line	embryonic stem cell
20	chr5:52407000-52410000	Weak transcription	Spleen	Spleen
21	chr5:52407000-52410200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
22	chr5:52407000-52410600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr5:52407000-52410600	Weak transcription	Dnd41	blood
24	chr5:52407000-52411800	Weak transcription	Brain Anterior Caudate	brain
25	chr5:52407000-52412200	Weak transcription	Primary T cells from cord blood	blood
26	chr5:52407000-52414800	Weak transcription	Pancreas	Pancrea
27	chr5:52407000-52418800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr5:52407000-52418800	Weak transcription	NHEK	skin
29	chr5:52407000-52419000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr5:52407200-52409800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr5:52407200-52410600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
32	chr5:52407200-52410600	Weak transcription	Brain Angular Gyrus	brain
33	chr5:52407200-52413400	Weak transcription	K562	blood
34	chr5:52407200-52418800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr5:52407800-52408400	Weak transcription	HepG2	liver

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