Variant report

Variant	rs715629
Chromosome Location	chr22:32806595-32806596
allele	A/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	POLR2A	chr22:32806138-32806964	GM12878	blood:	n/a	n/a
2	FOS	chr22:32806554-32806745	MCF10A-Er-Src	breast:	n/a	n/a
3	JUND	chr22:32806490-32806679	HepG2	liver:	n/a	chr22:32806622-32806633
4	TCF7L2	chr22:32806505-32806761	MCF-7	breast:	n/a	chr22:32806615-32806624 chr22:32806611-32806625
5	POLR2A	chr22:32806466-32806647	MCF10A-Er-Src	breast:	n/a	n/a
6	FOS	chr22:32806463-32806754	MCF10A-Er-Src	breast:	n/a	n/a
7	POLR2A	chr22:32806400-32806653	HepG2	liver:	n/a	n/a
8	MAFK	chr22:32806503-32806658	HepG2	liver:	n/a	chr22:32806622-32806632

No.	Distal block	Cell Line	Cell type
1	chr22:32806505..32810377-chr22:32871743..32874140,3	K562	blood:
2	chr22:32802183..32805062-chr22:32805761..32809013,3	MCF-7	breast:
3	chr22:32801191..32803610-chr22:32806296..32808272,2	K562	blood:

Variant related genes	Relation type
RTCB	TF binding region
ENSG00000100220	Chromatin interaction
ENSG00000100225	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs2072817	0.85[CHD][hapmap];0.81[ASN][1000 genomes]
rs2076042	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2076044	0.81[CEU][hapmap];0.90[CHB][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.95[ASN][1000 genomes]
rs2281036	0.86[LWK][hapmap];1.00[YRI][hapmap]
rs2413114	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs5749421	1.00[YRI][hapmap]
rs5749426	0.86[LWK][hapmap];0.88[YRI][hapmap]
rs5754063	0.84[YRI][hapmap]
rs5754066	1.00[YRI][hapmap]
rs9609537	0.93[ASW][hapmap];0.96[CEU][hapmap];0.80[CHB][hapmap];0.96[CHD][hapmap];0.93[GIH][hapmap];0.93[LWK][hapmap];0.94[MEX][hapmap];0.94[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9609538	0.93[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9619262	0.81[CHD][hapmap];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv459874	chr22:32574274-32866934	Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
2	nsv588895	chr22:32574274-32866934	Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
3	nsv1064737	chr22:32603912-32829725	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
4	nsv1066118	chr22:32779078-32815334	Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
5	nsv1055701	chr22:32806595-32845403	Weak transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs715629	PLA2G3	cis	cerebellum	SCAN
rs715629	C22orf28	cis	cerebellum	SCAN
rs715629	THOC5	cis	cerebellum	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:32781200-32806600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr22:32781400-32806600	Strong transcription	Placenta	Placenta
3	chr22:32782800-32807200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr22:32783200-32806600	Strong transcription	HUES48 Cell Line	embryonic stem cell
5	chr22:32794200-32807400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr22:32798000-32806800	Weak transcription	Psoas Muscle	Psoas
7	chr22:32802000-32806800	Genic enhancers	Primary B cells from cord blood	blood
8	chr22:32804200-32806600	Weak transcription	NHLF	lung
9	chr22:32804200-32806800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr22:32804200-32806800	Weak transcription	Esophagus	oesophagus
11	chr22:32804200-32807000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr22:32804200-32807600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr22:32804600-32807400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr22:32804800-32806600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr22:32804800-32807000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
16	chr22:32804800-32807000	Weak transcription	Primary neutrophils fromperipheralblood	blood
17	chr22:32805000-32806600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr22:32805000-32806600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
19	chr22:32805000-32806600	Weak transcription	Brain Germinal Matrix	brain
20	chr22:32805000-32806600	Enhancers	Pancreatic Islets	Pancreatic Islet
21	chr22:32805000-32806800	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr22:32805000-32806800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr22:32805000-32806800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
24	chr22:32805000-32806800	Weak transcription	Aorta	Aorta
25	chr22:32805000-32806800	Weak transcription	Fetal Intestine Large	intestine
26	chr22:32805000-32806800	Weak transcription	Lung	lung
27	chr22:32805000-32806800	Weak transcription	HSMM	muscle
28	chr22:32805000-32806800	Weak transcription	NH-A	brain
29	chr22:32805000-32807000	Weak transcription	H1 Cell Line	embryonic stem cell
30	chr22:32805200-32806600	Enhancers	Liver	Liver
31	chr22:32805400-32806600	Enhancers	Brain Hippocampus Middle	brain
32	chr22:32805600-32806600	Genic enhancers	Fetal Brain Female	brain
33	chr22:32805600-32806800	Enhancers	Primary T helper cells fromperipheralblood	blood
34	chr22:32805600-32807000	Enhancers	Stomach Mucosa	stomach
35	chr22:32806000-32806600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr22:32806000-32806600	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr22:32806000-32806600	Enhancers	Brain Inferior Temporal Lobe	brain
38	chr22:32806000-32806600	Enhancers	Fetal Brain Male	brain
39	chr22:32806000-32806600	Genic enhancers	Fetal Muscle Trunk	muscle
40	chr22:32806000-32806600	Transcr. at gene 5' and 3'	Dnd41	blood
41	chr22:32806000-32806800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
42	chr22:32806000-32806800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
43	chr22:32806000-32806800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
44	chr22:32806000-32806800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
45	chr22:32806000-32806800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
46	chr22:32806000-32806800	Enhancers	Right Ventricle	heart
47	chr22:32806000-32806800	Enhancers	Hela-S3	cervix
48	chr22:32806000-32807000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr22:32806000-32807000	Enhancers	Primary B cells from peripheral blood	blood
50	chr22:32806000-32807000	Enhancers	Primary T cells fromperipheralblood	blood

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