Variant report

Variant	rs7287918
Chromosome Location	chr22:29281710-29281711
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr22:29280249..29282213-chr22:29433685..29436671,2	MCF-7	breast:
2	chr22:29280662..29283145-chr22:29436035..29437760,2	K562	blood:
3	chr22:29279568..29281765-chr22:29467462..29470387,2	K562	blood:
4	chr22:29280624..29284164-chr22:29307760..29311501,3	MCF-7	breast:
5	chr22:29194507..29196726-chr22:29278986..29282462,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000100219	Chromatin interaction
ENSG00000183762	Chromatin interaction
ENSG00000226471	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs1065497	0.94[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs12165962	0.82[CEU][hapmap];0.84[JPT][hapmap];0.81[MEX][hapmap]
rs1318025	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1318026	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs132528	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs132529	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs132531	1.00[CEU][hapmap];0.90[CHB][hapmap];0.98[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs132533	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];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs132534	0.83[ASW][hapmap]
rs132536	0.96[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs132543	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs132548	1.00[CEU][hapmap];0.86[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2015500	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2064261	0.94[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];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2097461	0.89[JPT][hapmap]
rs2213645	0.95[JPT][hapmap]
rs2239815	0.83[CEU][hapmap];0.89[JPT][hapmap];0.95[MEX][hapmap];0.81[TSI][hapmap]
rs2239828	0.96[CEU][hapmap]
rs2269577	0.89[JPT][hapmap]
rs2347447	0.89[JPT][hapmap];0.95[MEX][hapmap];0.81[TSI][hapmap]
rs3788409	0.89[JPT][hapmap];0.95[MEX][hapmap];0.81[TSI][hapmap]
rs469990	0.96[CEU][hapmap];0.85[CHB][hapmap];0.95[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs469991	0.96[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs469992	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4822998	0.94[JPT][hapmap]
rs5752809	0.89[JPT][hapmap]
rs5752812	0.89[JPT][hapmap]
rs5752826	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs5762784	0.89[JPT][hapmap];0.86[MEX][hapmap]
rs5762788	0.89[JPT][hapmap];0.95[MEX][hapmap]
rs5762795	0.83[CEU][hapmap];0.89[JPT][hapmap];0.95[MEX][hapmap];0.81[TSI][hapmap]
rs5762870	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs5762874	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs5762877	0.87[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs5762880	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5762881	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs5762882	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];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5762936	0.95[JPT][hapmap]
rs5997408	0.83[CEU][hapmap];0.89[JPT][hapmap]
rs5997412	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6005881	0.89[JPT][hapmap];0.90[MEX][hapmap]
rs6005915	0.82[CHB][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap]
rs6005936	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6519766	0.89[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs715531	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7287806	0.83[CEU][hapmap];0.89[JPT][hapmap];0.95[MEX][hapmap];0.81[TSI][hapmap]
rs763073	0.83[CEU][hapmap];0.89[JPT][hapmap];0.95[MEX][hapmap];0.81[TSI][hapmap]
rs8136297	0.82[EUR][1000 genomes]
rs8137262	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8142067	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9620841	0.89[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9625619	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1064079	chr22:29065528-29456059	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
2	nsv834169	chr22:29095446-29303929	Weak transcription Active TSS Flanking Active TSS Genic enhancers Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
3	nsv531586	chr22:29252132-29902266	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
4	nsv3589	chr22:29265164-29288935	Enhancers Active TSS Bivalent Enhancer Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs7287918	MN1	cis	cerebellum	SCAN
rs7287918	ZNRF3	cis	parietal	SCAN
rs7287918	GAL3ST1	cis	cerebellum	SCAN
rs7287918	XBP1	Cis_1M	lymphoblastoid	RTeQTL
rs7287918	XBP1	cis	cerebellum	SCAN

Chromatin state (count:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:29278600-29282600	Active TSS	Brain Anterior Caudate	brain
2	chr22:29278800-29281800	Active TSS	Fetal Kidney	kidney
3	chr22:29279000-29282000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr22:29280200-29282200	Bivalent/Poised TSS	HepG2	liver
5	chr22:29280400-29282000	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr22:29280400-29282200	Flanking Active TSS	Liver	Liver
7	chr22:29280400-29282200	Flanking Active TSS	HMEC	breast
8	chr22:29280600-29281800	Flanking Active TSS	Fetal Lung	lung
9	chr22:29280600-29281800	Flanking Active TSS	NHEK	skin
10	chr22:29280600-29282000	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
11	chr22:29280600-29283600	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr22:29280800-29281800	Flanking Active TSS	Fetal Intestine Large	intestine
13	chr22:29280800-29282200	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr22:29281000-29282000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr22:29281000-29282400	Active TSS	Rectal Mucosa Donor 29	rectum
16	chr22:29281000-29287600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr22:29281200-29282000	Enhancers	Skeletal Muscle Male	skeletal muscle
18	chr22:29281200-29282200	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
19	chr22:29281200-29282200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr22:29281200-29282200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr22:29281200-29282200	Enhancers	Esophagus	oesophagus
22	chr22:29281200-29282200	Enhancers	Fetal Heart	heart
23	chr22:29281200-29282200	Enhancers	Right Ventricle	heart
24	chr22:29281200-29282400	Enhancers	NH-A	brain
25	chr22:29281200-29282600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
26	chr22:29281200-29283000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
27	chr22:29281200-29287400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr22:29281200-29288000	Weak transcription	Sigmoid Colon	Sigmoid Colon
29	chr22:29281400-29281800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr22:29281400-29281800	Active TSS	Fetal Brain Female	brain
31	chr22:29281400-29281800	Active TSS	Placenta	Placenta
32	chr22:29281400-29282000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr22:29281400-29282000	Enhancers	Fetal Brain Male	brain
34	chr22:29281400-29282000	Weak transcription	Pancreatic Islets	Pancreatic Islet
35	chr22:29281400-29282000	Weak transcription	Gastric	stomach
36	chr22:29281400-29282200	Enhancers	H9 Cell Line	embryonic stem cell
37	chr22:29281400-29282200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr22:29281400-29282200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr22:29281400-29282200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr22:29281400-29282200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr22:29281400-29282200	Enhancers	Adipose Nuclei	Adipose
42	chr22:29281400-29282200	Enhancers	Brain Substantia Nigra	brain
43	chr22:29281400-29282200	Enhancers	Rectal Smooth Muscle	rectum
44	chr22:29281400-29282200	Weak transcription	Right Atrium	heart
45	chr22:29281400-29282200	Enhancers	NHLF	lung
46	chr22:29281400-29282400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
47	chr22:29281400-29282400	Active TSS	Brain Inferior Temporal Lobe	brain
48	chr22:29281400-29282400	Enhancers	Duodenum Smooth Muscle	Duodenum
49	chr22:29281400-29282400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
50	chr22:29281400-29282400	Enhancers	A549	lung

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