Variant report

Variant	rs12165962
Chromosome Location	chr22:29188987-29188988
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 36 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs132531	0.82[CEU][hapmap];0.84[JPT][hapmap];0.80[YRI][hapmap]
rs132533	0.82[CEU][hapmap];0.84[JPT][hapmap]
rs132534	0.82[CEU][hapmap];0.82[TSI][hapmap]
rs132536	0.84[JPT][hapmap]
rs132539	0.82[TSI][hapmap]
rs132548	0.82[CEU][hapmap];0.84[JPT][hapmap];0.95[YRI][hapmap]
rs2064261	0.82[CEU][hapmap];0.84[JPT][hapmap];0.81[MEX][hapmap]
rs2097461	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs2239815	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.86[LWK][hapmap];0.85[MEX][hapmap];0.92[MKK][hapmap];0.97[TSI][hapmap];0.80[YRI][hapmap]
rs2269577	0.95[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs2347447	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.85[MEX][hapmap];0.97[TSI][hapmap]
rs3788409	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.85[MEX][hapmap];0.97[TSI][hapmap]
rs469989	0.81[CEU][hapmap]
rs469990	0.84[JPT][hapmap]
rs469991	0.84[JPT][hapmap]
rs5752809	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs5752812	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs5762784	0.95[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.81[MEX][hapmap];0.90[TSI][hapmap]
rs5762788	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.85[MEX][hapmap];0.92[TSI][hapmap]
rs5762795	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];0.85[MEX][hapmap];0.93[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap]
rs5762874	0.82[CEU][hapmap];0.84[JPT][hapmap]
rs5762881	0.82[CEU][hapmap];0.84[JPT][hapmap]
rs5762882	0.82[CEU][hapmap];0.84[JPT][hapmap]
rs5997408	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.95[YRI][hapmap]
rs6005881	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.93[LWK][hapmap];0.80[MEX][hapmap];0.95[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap]
rs6005915	0.86[CHB][hapmap];0.89[JPT][hapmap];0.85[TSI][hapmap]
rs6519766	0.83[ASW][hapmap];0.82[CEU][hapmap];0.84[JPT][hapmap];0.81[MEX][hapmap]
rs7287806	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.96[LWK][hapmap];0.85[MEX][hapmap];0.98[MKK][hapmap];0.97[TSI][hapmap];0.95[YRI][hapmap]
rs7287918	0.82[CEU][hapmap];0.84[JPT][hapmap];0.81[MEX][hapmap]
rs763073	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.83[LWK][hapmap];0.85[MEX][hapmap];0.92[MKK][hapmap];0.97[TSI][hapmap];0.80[YRI][hapmap]
rs9620841	0.83[ASW][hapmap];0.82[CEU][hapmap];0.84[JPT][hapmap];0.81[MEX][hapmap]
rs9625619	0.82[CEU][hapmap];0.84[JPT][hapmap]

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	nsv916473	chr22:28837041-29215603	Weak transcription Bivalent Enhancer Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
2	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
3	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
4	esv1314301	chr22:29188986-29188987	Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs12165962	MN1	cis	cerebellum	SCAN
rs12165962	XBP1	cis	cerebellum	SCAN
rs12165962	BEND4	trans	parietal	SCAN
rs12165962	SEZ6L	cis	cerebellum	SCAN
rs12165962	GAL3ST1	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:29169800-29190400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr22:29170000-29190200	Weak transcription	Fetal Heart	heart
3	chr22:29170000-29194200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr22:29173800-29193000	Weak transcription	Right Atrium	heart
5	chr22:29176800-29190200	Weak transcription	Hela-S3	cervix
6	chr22:29180400-29191000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr22:29180600-29191000	Weak transcription	Small Intestine	intestine
8	chr22:29180800-29189800	Weak transcription	HMEC	breast
9	chr22:29180800-29190200	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr22:29181600-29191000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr22:29182000-29191000	Weak transcription	Fetal Brain Male	brain
12	chr22:29182400-29190000	Weak transcription	Stomach Mucosa	stomach
13	chr22:29182400-29190000	Weak transcription	HSMMtube	muscle
14	chr22:29182400-29190000	Weak transcription	NHEK	skin
15	chr22:29182400-29190200	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr22:29182400-29190800	Weak transcription	Gastric	stomach
17	chr22:29182400-29191200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr22:29182600-29189800	Weak transcription	NHLF	lung
19	chr22:29182600-29190200	Weak transcription	A549	lung
20	chr22:29182600-29190800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr22:29182600-29191000	Weak transcription	Ovary	ovary
22	chr22:29182600-29191200	Weak transcription	Esophagus	oesophagus
23	chr22:29182800-29190000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr22:29182800-29190000	Weak transcription	Right Ventricle	heart
25	chr22:29182800-29190400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
26	chr22:29183000-29190000	Weak transcription	Brain Anterior Caudate	brain
27	chr22:29183000-29190000	Weak transcription	Fetal Kidney	kidney
28	chr22:29183000-29190000	Weak transcription	Rectal Smooth Muscle	rectum
29	chr22:29183000-29190200	Weak transcription	K562	blood
30	chr22:29183200-29189200	Weak transcription	Muscle Satellite Cultured Cells	--
31	chr22:29183200-29189800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr22:29183200-29190000	Weak transcription	Brain Substantia Nigra	brain
33	chr22:29183400-29190000	Weak transcription	Psoas Muscle	Psoas
34	chr22:29183600-29190000	Weak transcription	H1 Cell Line	embryonic stem cell
35	chr22:29183600-29190200	Genic enhancers	Dnd41	blood
36	chr22:29183600-29191000	Weak transcription	Spleen	Spleen
37	chr22:29183800-29189000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr22:29183800-29190000	Weak transcription	Cortex derived primary cultured neurospheres	brain
39	chr22:29183800-29190200	Weak transcription	Colonic Mucosa	Colon
40	chr22:29183800-29191000	Weak transcription	Aorta	Aorta
41	chr22:29184000-29190000	Weak transcription	Placenta Amnion	Placenta Amnion
42	chr22:29184200-29190600	Weak transcription	Brain Germinal Matrix	brain
43	chr22:29184400-29189800	Weak transcription	Skeletal Muscle Male	skeletal muscle
44	chr22:29184400-29190000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
45	chr22:29184400-29190000	Weak transcription	Brain Angular Gyrus	brain
46	chr22:29184400-29190000	Weak transcription	Brain Inferior Temporal Lobe	brain
47	chr22:29184400-29190000	Weak transcription	HUVEC	blood vessel
48	chr22:29184600-29189800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
49	chr22:29184600-29190000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr22:29184800-29189000	Weak transcription	Sigmoid Colon	Sigmoid Colon

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