Variant report

Variant	rs1034589
Chromosome Location	chr22:31579233-31579234
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 63 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs1034588	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13056485	0.90[CHB][hapmap];0.88[JPT][hapmap]
rs13158	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.91[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];0.84[ASN][1000 genomes]
rs1858821	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.91[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];1.00[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs2040533	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs2073857	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.91[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];1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2078803	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes]
rs2079431	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2106294	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.91[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];1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2228619	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2232170	0.85[CEU][hapmap]
rs2232176	0.85[CEU][hapmap]
rs2283879	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2283881	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2413031	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2413032	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2413033	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2413034	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2413035	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.91[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];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2413045	1.00[MKK][hapmap]
rs2413046	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2413047	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2413049	0.85[EUR][1000 genomes]
rs4141404	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.91[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];1.00[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs4299418	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4603880	1.00[ASW][hapmap];1.00[CEU][hapmap];0.82[CHB][hapmap];0.86[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.81[EUR][1000 genomes]
rs4820042	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4820043	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.91[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];1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4820951	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4820955	1.00[CEU][hapmap]
rs4820962	0.81[EUR][1000 genomes]
rs4820963	1.00[CEU][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs5749224	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5749229	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.91[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];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs5753500	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs5753505	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs5753507	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs5753521	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs5753543	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes]
rs5997893	0.90[MEX][hapmap]
rs5997902	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs5997912	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs5997913	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs5997933	0.85[EUR][1000 genomes]
rs5997939	1.00[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs714909	1.00[ASW][hapmap];1.00[CEU][hapmap];0.82[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.81[EUR][1000 genomes]
rs715510	1.00[CEU][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs7287267	0.81[EUR][1000 genomes]
rs737684	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes]
rs737887	1.00[ASW][hapmap];1.00[CEU][hapmap];0.82[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.83[EUR][1000 genomes]
rs737888	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8135344	1.00[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs8135347	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8135417	0.90[MEX][hapmap]
rs9606830	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap]
rs9606831	0.81[EUR][1000 genomes]
rs9609264	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes]
rs9609265	0.81[EUR][1000 genomes]
rs9609266	0.81[EUR][1000 genomes]
rs9609267	0.80[EUR][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	nsv459871	chr22:31551160-31680624	Weak transcription Genic enhancers Enhancers Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	23 gene(s)	inside rSNPs	diseases
2	nsv588893	chr22:31551160-31680624	Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	23 gene(s)	inside rSNPs	diseases
3	nsv1067003	chr22:31558663-31697093	Enhancers Genic enhancers Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs1034589	MN1	cis	parietal	SCAN
rs1034589	SFI1	cis	cerebellum	SCAN
rs1034589	MGC17330	cis	multi-tissue	Pritchard
rs1034589	SFI1	cis	Thyroid	GTEx
rs1034589	PISD	cis	cerebellum	SCAN
rs1034589	RHBDD3	cis	cerebellum	SCAN

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:31557200-31591200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr22:31557400-31579800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr22:31557400-31595200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
4	chr22:31557400-31597800	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr22:31557600-31591800	Weak transcription	HUES48 Cell Line	embryonic stem cell
6	chr22:31557800-31587000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
7	chr22:31557800-31588400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr22:31558600-31583000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
9	chr22:31558600-31591400	Weak transcription	Primary hematopoietic stem cells	blood
10	chr22:31558800-31591200	Weak transcription	Fetal Brain Male	brain
11	chr22:31558800-31606000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
12	chr22:31562400-31583200	Weak transcription	HUES64 Cell Line	embryonic stem cell
13	chr22:31564600-31582600	Weak transcription	Fetal Thymus	thymus
14	chr22:31566200-31583000	Weak transcription	Brain Angular Gyrus	brain
15	chr22:31566400-31583000	Weak transcription	Brain Cingulate Gyrus	brain
16	chr22:31569600-31583200	Weak transcription	Brain Anterior Caudate	brain
17	chr22:31569800-31583000	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr22:31569800-31591600	Weak transcription	Small Intestine	intestine
19	chr22:31570000-31606400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
20	chr22:31570200-31583000	Weak transcription	Duodenum Smooth Muscle	Duodenum
21	chr22:31570400-31583000	Weak transcription	Rectal Smooth Muscle	rectum
22	chr22:31570400-31586800	Strong transcription	Fetal Stomach	stomach
23	chr22:31570400-31597800	Weak transcription	HUVEC	blood vessel
24	chr22:31571800-31582800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr22:31572200-31600000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr22:31572800-31579400	Strong transcription	Monocytes-CD14+_RO01746	blood
27	chr22:31573600-31583000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
28	chr22:31573600-31583000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
29	chr22:31574000-31583200	Weak transcription	Duodenum Mucosa	Duodenum
30	chr22:31574200-31590800	Weak transcription	Brain Substantia Nigra	brain
31	chr22:31574400-31581400	Weak transcription	Placenta	Placenta
32	chr22:31574400-31601600	Weak transcription	Fetal Heart	heart
33	chr22:31574600-31581000	Weak transcription	Fetal Lung	lung
34	chr22:31574600-31581200	Weak transcription	Primary neutrophils fromperipheralblood	blood
35	chr22:31574600-31583200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
36	chr22:31574800-31579800	Weak transcription	H1 Cell Line	embryonic stem cell
37	chr22:31574800-31581000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
38	chr22:31574800-31583000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr22:31574800-31587200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
40	chr22:31575200-31580000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
41	chr22:31575400-31582800	Weak transcription	Thymus	Thymus
42	chr22:31575600-31581200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
43	chr22:31575800-31579800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
44	chr22:31575800-31580200	Strong transcription	Fetal Intestine Small	intestine
45	chr22:31575800-31581000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
46	chr22:31575800-31581200	Weak transcription	Primary T helper cells fromperipheralblood	blood
47	chr22:31575800-31583000	Weak transcription	Adipose Nuclei	Adipose
48	chr22:31575800-31583000	Weak transcription	Aorta	Aorta
49	chr22:31575800-31583000	Weak transcription	HepG2	liver
50	chr22:31575800-31588600	Weak transcription	Colon Smooth Muscle	Colon

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