Variant report

Variant	rs4820048
Chromosome Location	chr22:31854370-31854371
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr22:31848344..31851110-chr22:31853744..31855617,2	K562	blood:
2	chr22:31850678..31853429-chr22:31854151..31856041,2	MCF-7	breast:
3	chr22:31853776..31856046-chr22:31858521..31860568,2	MCF-7	breast:
4	chr22:31853100..31854749-chr22:31856675..31859325,2	K562	blood:

Variant related genes	Relation type
ENSG00000184708	Chromatin interaction
ENSG00000224623	Chromatin interaction
ENSG00000240591	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs11704494	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12166373	0.82[MEX][hapmap]
rs131209	0.82[MEX][hapmap]
rs131213	0.82[MEX][hapmap]
rs1543416	0.87[LWK][hapmap];0.86[YRI][hapmap]
rs1916	1.00[ASW][hapmap];0.85[CEU][hapmap];0.82[CHB][hapmap];0.85[LWK][hapmap];0.87[MKK][hapmap];0.86[TSI][hapmap];0.90[YRI][hapmap]
rs2006771	0.85[CEU][hapmap];0.82[TSI][hapmap]
rs2012451	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.95[MEX][hapmap];0.98[MKK][hapmap];0.89[TSI][hapmap];0.86[YRI][hapmap];0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2103853	1.00[CHB][hapmap];0.89[JPT][hapmap]
rs28715	0.82[MEX][hapmap]
rs35143518	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4541328	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4820045	0.82[MEX][hapmap];0.80[TSI][hapmap]
rs4820974	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	0.83[LWK][hapmap];0.86[YRI][hapmap]
rs5753625	1.00[CHB][hapmap];0.89[JPT][hapmap]
rs5753630	1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs5994397	0.86[YRI][hapmap]
rs5997971	0.83[YRI][hapmap]
rs5997986	0.87[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs5997988	0.83[ASW][hapmap];1.00[CEU][hapmap];0.84[GIH][hapmap];0.93[LWK][hapmap];0.86[MEX][hapmap];0.86[MKK][hapmap];0.98[TSI][hapmap];0.86[YRI][hapmap];0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs5997989	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs5997990	0.87[AFR][1000 genomes]
rs5998002	1.00[ASW][hapmap];0.85[CEU][hapmap];0.82[CHB][hapmap];0.90[LWK][hapmap];0.91[MEX][hapmap];0.86[MKK][hapmap];0.89[TSI][hapmap];0.89[YRI][hapmap];0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs5998003	0.88[EUR][1000 genomes]
rs5998004	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs5998012	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs5998016	0.83[EUR][1000 genomes]
rs5998017	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs5998021	0.85[CEU][hapmap];0.86[EUR][1000 genomes]
rs6518745	0.95[LWK][hapmap];0.98[MKK][hapmap];0.86[YRI][hapmap]
rs7287937	0.85[CEU][hapmap];0.82[TSI][hapmap]
rs7289941	0.85[CEU][hapmap];0.93[TSI][hapmap];0.89[EUR][1000 genomes]
rs926928	0.95[LWK][hapmap];0.97[MKK][hapmap];0.81[TSI][hapmap];0.83[YRI][hapmap]
rs9609263	0.83[MEX][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	nsv834176	chr22:31682426-31864701	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	52 gene(s)	inside rSNPs	diseases
2	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
3	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
4	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
5	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
rs4820048	CRYBB1	cis	cerebellum	SCAN
rs4820048	DRG1	Cis_1M	lymphoblastoid	RTeQTL
rs4820048	LIMK2	cis	cerebellum	SCAN
rs4820048	MN1	cis	parietal	SCAN

Chromatin state (count:125 , 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	chr22:31797200-31860600	Strong transcription	Fetal Stomach	stomach
4	chr22:31815000-31868200	Strong transcription	Dnd41	blood
5	chr22:31815000-31883400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr22:31822400-31859800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr22:31823600-31884600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr22:31832600-31867800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr22:31836200-31873600	Weak transcription	Stomach Mucosa	stomach
10	chr22:31838200-31859000	Weak transcription	Hela-S3	cervix
11	chr22:31838600-31854400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr22:31840800-31857200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr22:31844600-31854400	Weak transcription	Psoas Muscle	Psoas
14	chr22:31844600-31857800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr22:31845000-31854400	Weak transcription	NHLF	lung
16	chr22:31845800-31860400	Strong transcription	Primary T cells from cord blood	blood
17	chr22:31846000-31865800	Strong transcription	Rectal Mucosa Donor 31	rectum
18	chr22:31846400-31854400	Weak transcription	Aorta	Aorta
19	chr22:31846400-31872000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
20	chr22:31847400-31856200	Strong transcription	Sigmoid Colon	Sigmoid Colon
21	chr22:31847600-31859800	Strong transcription	Placenta	Placenta
22	chr22:31847600-31860400	Strong transcription	Fetal Intestine Large	intestine
23	chr22:31847600-31881800	Strong transcription	Monocytes-CD14+_RO01746	blood
24	chr22:31847800-31860400	Strong transcription	Primary B cells from cord blood	blood
25	chr22:31847800-31868200	Strong transcription	Primary monocytes fromperipheralblood	blood
26	chr22:31848000-31865600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr22:31848000-31867400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr22:31848000-31868000	Strong transcription	Primary T helper cells PMA-I stimulated	--
29	chr22:31848000-31868400	Strong transcription	HUES64 Cell Line	embryonic stem cell
30	chr22:31848200-31856200	Strong transcription	Primary hematopoietic stem cells	blood
31	chr22:31848200-31856200	Strong transcription	NH-A	brain
32	chr22:31848200-31860200	Strong transcription	Adipose Nuclei	Adipose
33	chr22:31848200-31860200	Strong transcription	Brain Inferior Temporal Lobe	brain
34	chr22:31848200-31860200	Strong transcription	HUVEC	blood vessel
35	chr22:31848200-31860400	Strong transcription	Liver	Liver
36	chr22:31848200-31860400	Strong transcription	Duodenum Mucosa	Duodenum
37	chr22:31848200-31860400	Strong transcription	Rectal Mucosa Donor 29	rectum
38	chr22:31848200-31865800	Strong transcription	HUES6 Cell Line	embryonic stem cell
39	chr22:31848200-31867600	Strong transcription	Primary T cells fromperipheralblood	blood
40	chr22:31848200-31867800	Strong transcription	Primary B cells from peripheral blood	blood
41	chr22:31848200-31868200	Strong transcription	HUES48 Cell Line	embryonic stem cell
42	chr22:31848200-31868400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
43	chr22:31848400-31855600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
44	chr22:31848400-31855800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr22:31848400-31856400	Strong transcription	NHDF-Ad	bronchial
46	chr22:31848400-31860000	Strong transcription	Brain Anterior Caudate	brain
47	chr22:31848400-31860200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr22:31848400-31860400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr22:31848400-31860400	Strong transcription	Primary T helper cells fromperipheralblood	blood
50	chr22:31848400-31860400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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