Variant report

Variant	rs2064261
Chromosome Location	chr22:29287730-29287731
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr22:29278420..29281129-chr22:29285869..29288774,2	K562	blood:
2	chr22:29279139..29280999-chr22:29287403..29288921,2	K562	blood:
3	chr22:29283926..29288290-chr22:29291343..29295207,5	K562	blood:

Variant related genes	Relation type
ENSG00000183579	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:51)

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	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1318026	0.88[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];0.82[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];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
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]
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];0.83[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	1.00[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];0.92[YRI][hapmap];0.88[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];0.96[YRI][hapmap];0.97[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	0.83[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.89[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]
rs7287918	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]
rs763073	0.83[CEU][hapmap];0.89[JPT][hapmap];0.95[MEX][hapmap];0.81[TSI][hapmap]
rs8136297	0.82[EUR][1000 genomes]
rs8137262	0.88[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	0.83[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];0.89[YRI][hapmap];0.88[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];0.89[YRI][hapmap];0.86[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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2064261	GAL3ST1	cis	cerebellum	SCAN
rs2064261	MN1	cis	cerebellum	SCAN
rs2064261	ZNRF3	cis	parietal	SCAN
rs2064261	XBP1	cis	cerebellum	SCAN

Chromatin state (count:74 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:29281200-29288000	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr22:29281400-29288000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr22:29281400-29288000	Weak transcription	Lung	lung
4	chr22:29281400-29290400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr22:29281400-29290400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr22:29281400-29290400	Weak transcription	Fetal Muscle Trunk	muscle
7	chr22:29281400-29290400	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr22:29281400-29294600	Weak transcription	Muscle Satellite Cultured Cells	--
9	chr22:29281400-29295200	Weak transcription	Brain Hippocampus Middle	brain
10	chr22:29281600-29292600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr22:29282000-29290400	Weak transcription	Brain Cingulate Gyrus	brain
12	chr22:29282000-29291400	Enhancers	Breast Myoepithelial Primary Cells	Breast
13	chr22:29282200-29287800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr22:29282200-29288000	Weak transcription	Right Ventricle	heart
15	chr22:29282200-29288200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr22:29282200-29290400	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr22:29282200-29295000	Weak transcription	Brain Substantia Nigra	brain
18	chr22:29282400-29287800	Weak transcription	Duodenum Smooth Muscle	Duodenum
19	chr22:29282400-29288000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr22:29282400-29290400	Weak transcription	Brain Inferior Temporal Lobe	brain
21	chr22:29283000-29287800	Weak transcription	Rectal Mucosa Donor 31	rectum
22	chr22:29283000-29288000	Weak transcription	Esophagus	oesophagus
23	chr22:29283000-29288000	Weak transcription	Gastric	stomach
24	chr22:29283200-29288200	Weak transcription	Rectal Mucosa Donor 29	rectum
25	chr22:29283400-29288000	Weak transcription	K562	blood
26	chr22:29283400-29294200	Weak transcription	Aorta	Aorta
27	chr22:29283400-29299000	Weak transcription	Fetal Stomach	stomach
28	chr22:29283800-29290200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr22:29284000-29287800	Weak transcription	Fetal Intestine Small	intestine
30	chr22:29284200-29288200	Weak transcription	Colon Smooth Muscle	Colon
31	chr22:29284200-29290400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
32	chr22:29284200-29292600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
33	chr22:29284400-29287800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
34	chr22:29284400-29287800	Weak transcription	Fetal Intestine Large	intestine
35	chr22:29284400-29287800	Weak transcription	Fetal Kidney	kidney
36	chr22:29284400-29288000	Weak transcription	Brain Anterior Caudate	brain
37	chr22:29284400-29288200	Weak transcription	Adipose Nuclei	Adipose
38	chr22:29284600-29288000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr22:29285800-29287800	Weak transcription	Fetal Lung	lung
40	chr22:29285800-29288000	Weak transcription	Duodenum Mucosa	Duodenum
41	chr22:29286000-29287800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr22:29286000-29299000	Weak transcription	Ovary	ovary
43	chr22:29286200-29291600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
44	chr22:29286400-29290400	Weak transcription	Right Atrium	heart
45	chr22:29286800-29287800	Weak transcription	Brain Germinal Matrix	brain
46	chr22:29286800-29288400	Enhancers	Cortex derived primary cultured neurospheres	brain
47	chr22:29286800-29297800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr22:29287000-29288000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
49	chr22:29287000-29288600	Enhancers	Liver	Liver
50	chr22:29287000-29288800	Enhancers	Fetal Heart	heart

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