Variant report

Variant	rs4820974
Chromosome Location	chr22:31869467-31869468
allele	A/C
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: 32 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs11704494	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1543416	0.87[LWK][hapmap];0.83[MKK][hapmap];0.82[YRI][hapmap]
rs1916	0.94[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];0.88[LWK][hapmap];0.91[MKK][hapmap];0.84[TSI][hapmap];0.93[YRI][hapmap]
rs2006771	0.89[CEU][hapmap];0.80[TSI][hapmap]
rs2012451	0.92[CEU][hapmap];0.82[CHB][hapmap];0.94[CHD][hapmap];0.95[GIH][hapmap];0.95[LWK][hapmap];0.91[MEX][hapmap];0.94[MKK][hapmap];0.87[TSI][hapmap];0.83[YRI][hapmap];0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2103853	0.82[CHB][hapmap]
rs35143518	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4541328	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4820048	0.94[ASW][hapmap];0.96[CEU][hapmap];0.82[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.97[LWK][hapmap];0.95[MEX][hapmap];0.96[MKK][hapmap];0.98[TSI][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4820983	0.80[LWK][hapmap];0.83[MKK][hapmap];0.82[YRI][hapmap]
rs5753625	0.82[CHB][hapmap]
rs5753630	0.82[CHB][hapmap];0.82[CHD][hapmap]
rs5994397	0.83[YRI][hapmap]
rs5997986	0.82[AFR][1000 genomes]
rs5997988	0.96[CEU][hapmap];0.85[GIH][hapmap];0.90[LWK][hapmap];0.82[MEX][hapmap];0.87[MKK][hapmap];0.96[TSI][hapmap];0.83[YRI][hapmap];0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs5997989	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs5997990	0.81[AFR][1000 genomes]
rs5998002	0.94[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.95[MEX][hapmap];0.90[MKK][hapmap];0.87[TSI][hapmap];0.93[YRI][hapmap];0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs5998003	0.91[EUR][1000 genomes]
rs5998004	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs5998012	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs5998016	0.86[EUR][1000 genomes]
rs5998017	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs5998021	0.89[CEU][hapmap];0.89[EUR][1000 genomes]
rs6518745	0.93[LWK][hapmap];0.94[MKK][hapmap];0.83[YRI][hapmap]
rs7287937	0.89[CEU][hapmap];0.80[TSI][hapmap]
rs7289941	0.89[CEU][hapmap];0.91[TSI][hapmap];0.92[EUR][1000 genomes]
rs926928	0.92[LWK][hapmap];0.93[MKK][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	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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4820974	MN1	cis	parietal	SCAN
rs4820974	DRG1	Cis_1M	lymphoblastoid	RTeQTL
rs4820974	CRYBB1	cis	cerebellum	SCAN
rs4820974	LIMK2	cis	cerebellum	SCAN

Chromatin state (count:126 , 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	chr22:31865400-31869800	Weak transcription	Primary B cells from cord blood	blood
42	chr22:31865400-31873600	Weak transcription	Stomach Smooth Muscle	stomach
43	chr22:31865400-31877000	Weak transcription	H1 Cell Line	embryonic stem cell
44	chr22:31865600-31870800	Weak transcription	Brain Germinal Matrix	brain
45	chr22:31865600-31873400	Weak transcription	Brain Inferior Temporal Lobe	brain
46	chr22:31865600-31876000	Weak transcription	Fetal Lung	lung
47	chr22:31865600-31877200	Weak transcription	K562	blood
48	chr22:31865600-31877200	Weak transcription	NHLF	lung
49	chr22:31865800-31871000	Weak transcription	Fetal Brain Female	brain
50	chr22:31865800-31871400	Weak transcription	Ovary	ovary

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