Variant report

Variant	rs5753639
Chromosome Location	chr22:31870400-31870401
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	22:31864703-31891033..22:31936958-31958600	GM12878	blood:
2	22:31864703-31891033..22:31930706-31935473	GM12878	blood:
3	22:31864703-31891033..22:32347255-32351014	K562	blood:

Variant related genes	Relation type
ENSG00000214093	Chromatin interaction
ENSG00000229169	Chromatin interaction
ENSG00000238910	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs1001599	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10483159	0.89[LWK][hapmap]
rs12485048	0.83[LWK][hapmap]
rs13057504	0.85[EUR][1000 genomes]
rs1858821	0.95[CEU][hapmap];0.85[TSI][hapmap]
rs2040533	0.95[CEU][hapmap]
rs2103853	0.94[LWK][hapmap];0.98[MKK][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes]
rs2273249	1.00[CEU][hapmap];0.81[JPT][hapmap];0.85[EUR][1000 genomes]
rs2273251	1.00[CEU][hapmap];0.86[JPT][hapmap];0.85[EUR][1000 genomes]
rs2899164	1.00[CEU][hapmap]
rs4141404	0.95[CEU][hapmap];0.85[TSI][hapmap]
rs4603880	0.95[CEU][hapmap];0.88[TSI][hapmap]
rs4820963	0.95[CEU][hapmap]
rs5749279	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs5749286	0.80[CEU][hapmap];0.82[TSI][hapmap]
rs5749298	0.80[CEU][hapmap]
rs5753543	0.95[CEU][hapmap]
rs5753601	1.00[CEU][hapmap];0.81[JPT][hapmap]
rs5753609	0.83[ASW][hapmap];0.95[CEU][hapmap];0.87[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.86[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs5753615	0.84[EUR][1000 genomes]
rs5753618	0.86[JPT][hapmap]
rs5753621	0.85[JPT][hapmap];0.87[EUR][1000 genomes]
rs5753625	0.94[LWK][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes]
rs5753628	0.88[EUR][1000 genomes]
rs5753630	0.80[LWK][hapmap]
rs5753631	0.93[EUR][1000 genomes]
rs5753632	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.95[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs5753648	0.80[EUR][1000 genomes]
rs5753659	0.82[TSI][hapmap]
rs5753669	0.80[CEU][hapmap];0.82[TSI][hapmap]
rs5753671	0.80[CEU][hapmap];0.82[TSI][hapmap]
rs5753698	0.80[CEU][hapmap]
rs5998058	0.80[CEU][hapmap]
rs5998067	0.80[CEU][hapmap]
rs695438	0.87[CHB][hapmap];0.91[JPT][hapmap]
rs714909	0.95[CEU][hapmap];0.88[TSI][hapmap]
rs715510	0.95[CEU][hapmap]
rs7284622	0.80[CEU][hapmap]
rs7285619	1.00[CEU][hapmap];0.82[GIH][hapmap];0.86[JPT][hapmap];0.91[TSI][hapmap];0.87[EUR][1000 genomes]
rs737887	0.95[CEU][hapmap];0.85[TSI][hapmap]
rs738657	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8138525	0.80[CEU][hapmap]
rs8139625	0.84[EUR][1000 genomes]
rs9606830	0.95[CEU][hapmap]
rs9606839	1.00[CEU][hapmap];0.82[GIH][hapmap];0.86[JPT][hapmap];0.91[TSI][hapmap]
rs9606843	1.00[CEU][hapmap];0.84[GIH][hapmap];0.86[JPT][hapmap];0.88[TSI][hapmap];0.88[EUR][1000 genomes]
rs9606848	0.82[TSI][hapmap]
rs9609264	0.95[CEU][hapmap]
rs9609286	0.85[EUR][1000 genomes]
rs9609296	0.80[CEU][hapmap];0.85[TSI][hapmap]
rs9609297	0.80[CEU][hapmap]
rs9609304	0.80[CEU][hapmap];0.82[TSI][hapmap]
rs9609329	0.80[CEU][hapmap]

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	nsv1063634	chr22:31797004-31921254	Strong transcription Weak transcription Enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
2	nsv459872	chr22:31833759-31977594	Strong transcription Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases
3	nsv588894	chr22:31833759-31977594	Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases
4	esv1791934	chr22:31846234-31874194	Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Enhancers Flanking Active TSS	TF binding region Chromatin interactive region	18 gene(s)	inside rSNPs	diseases
5	nsv1060776	chr22:31869892-31900359	Active TSS Transcr. at gene 5' and 3' Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs5753639	SFI1	cis	cerebellum	SCAN
rs5753639	MN1	cis	parietal	SCAN
rs5753639	DRG1	Cis_1M	lymphoblastoid	RTeQTL
rs5753639	PISD	cis	cerebellum	SCAN
rs5753639	SFI1	cis	Thyroid	GTEx

Chromatin state (count:129 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:31797000-31884400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr22:31797000-31884400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr22:31815000-31883400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr22:31823600-31884600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr22:31836200-31873600	Weak transcription	Stomach Mucosa	stomach
6	chr22:31846400-31872000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
7	chr22:31847600-31881800	Strong transcription	Monocytes-CD14+_RO01746	blood
8	chr22:31848800-31883000	Weak transcription	Fetal Heart	heart
9	chr22:31850200-31871400	Strong transcription	GM12878-XiMat	blood
10	chr22:31850800-31876800	Weak transcription	Esophagus	oesophagus
11	chr22:31854800-31884600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr22:31856800-31885000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr22:31858200-31877800	Weak transcription	Fetal Brain Male	brain
14	chr22:31858400-31884600	Weak transcription	Psoas Muscle	Psoas
15	chr22:31859000-31875200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
16	chr22:31859200-31873600	Weak transcription	A549	lung
17	chr22:31859400-31871800	Weak transcription	Hela-S3	cervix
18	chr22:31859400-31873800	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr22:31859400-31883800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
20	chr22:31859400-31884800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr22:31859800-31873600	Weak transcription	Pancreatic Islets	Pancreatic Islet
22	chr22:31860000-31873800	Weak transcription	Colonic Mucosa	Colon
23	chr22:31860000-31882600	Weak transcription	Skeletal Muscle Male	skeletal muscle
24	chr22:31860200-31875800	Weak transcription	Brain Angular Gyrus	brain
25	chr22:31860200-31884800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
26	chr22:31861200-31871400	Strong transcription	Primary T cells from cord blood	blood
27	chr22:31861600-31873600	Weak transcription	NHEK	skin
28	chr22:31863000-31877600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
29	chr22:31863400-31879400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
30	chr22:31864000-31875000	Weak transcription	Fetal Kidney	kidney
31	chr22:31864200-31875600	Weak transcription	HMEC	breast
32	chr22:31864400-31877600	Weak transcription	Small Intestine	intestine
33	chr22:31864400-31879800	Weak transcription	Placenta Amnion	Placenta Amnion
34	chr22:31864400-31884400	Weak transcription	Brain Substantia Nigra	brain
35	chr22:31864400-31884600	Weak transcription	Aorta	Aorta
36	chr22:31864600-31884600	Weak transcription	Right Ventricle	heart
37	chr22:31864800-31870800	Weak transcription	Rectal Smooth Muscle	rectum
38	chr22:31864800-31873600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
39	chr22:31865000-31873600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr22:31865200-31876800	Weak transcription	Gastric	stomach
41	chr22:31865400-31873600	Weak transcription	Stomach Smooth Muscle	stomach
42	chr22:31865400-31877000	Weak transcription	H1 Cell Line	embryonic stem cell
43	chr22:31865600-31870800	Weak transcription	Brain Germinal Matrix	brain
44	chr22:31865600-31873400	Weak transcription	Brain Inferior Temporal Lobe	brain
45	chr22:31865600-31876000	Weak transcription	Fetal Lung	lung
46	chr22:31865600-31877200	Weak transcription	K562	blood
47	chr22:31865600-31877200	Weak transcription	NHLF	lung
48	chr22:31865800-31871000	Weak transcription	Fetal Brain Female	brain
49	chr22:31865800-31871400	Weak transcription	Ovary	ovary
50	chr22:31865800-31873600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood

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