Variant report

Variant	rs4820834
Chromosome Location	chr22:30751627-30751628
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:4)
CpG islands
(count:0)
Chromatin interactive
region (count:14)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:4 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	WRNIP1	chr22:30751598-30751664	GM12878	blood:	n/a	n/a
2	POLR2A	chr22:30751204-30751808	GM12892	blood:	n/a	n/a
3	POLR2A	chr22:30750048-30751795	GM12878	blood:	n/a	n/a
4	POLR2A	chr22:30751154-30751795	GM12878	blood:	n/a	n/a

No data

(count:14 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr22:30740000..30742543-chr22:30750600..30752817,3	MCF-7	breast:
2	chr22:30722006..30725049-chr22:30749886..30754508,5	K562	blood:
3	chr22:30736285..30738437-chr22:30751447..30754136,2	K562	blood:
4	chr22:30682051..30684043-chr22:30751437..30753247,3	MCF-7	breast:
5	chr22:30720936..30724991-chr22:30750350..30754449,10	MCF-7	breast:
6	chr22:30679588..30687274-chr22:30748772..30756086,11	MCF-7	breast:
7	chr22:30681963..30685470-chr22:30751422..30755510,6	K562	blood:
8	chr22:30750563..30752352-chr22:30759520..30761812,2	MCF-7	breast:
9	chr22:30719395..30724233-chr22:30750032..30754717,7	MCF-7	breast:
10	chr22:30681129..30691076-chr22:30751303..30759078,14	K562	blood:
11	chr22:30742977..30744840-chr22:30750667..30752552,2	K562	blood:
12	chr22:30750108..30752468-chr22:30775828..30777865,2	MCF-7	breast:
13	chr22:30736285..30738543-chr22:30751447..30754136,3	K562	blood:
14	chr22:30732348..30737677-chr22:30750921..30755238,7	MCF-7	breast:

No data

Variant related genes	Relation type
CCDC157	TF binding region
ENSG00000099995	Chromatin interaction
ENSG00000099992	Chromatin interaction
ENSG00000239282	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs13056562	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13058084	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13058399	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13058535	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs17730748	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17738020	1.00[ASW][hapmap];1.00[MKK][hapmap];1.00[ASN][1000 genomes]
rs34102711	1.00[ASN][1000 genomes]
rs34318316	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34911581	1.00[AFR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34964064	1.00[AFR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35074129	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs35246430	1.00[ASN][1000 genomes]
rs35617977	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs35960997	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4449240	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4820002	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4820840	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4823086	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4823087	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67401267	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs68042293	1.00[ASN][1000 genomes]
rs73168654	1.00[ASN][1000 genomes]

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	nsv829171	chr22:30598030-31043578	Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
2	nsv914970	chr22:30619599-30850395	Active TSS Enhancers Genic enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
3	nsv915818	chr22:30708245-31346302	Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
4	nsv1066179	chr22:30724148-30766466	Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Coronary artery calcification	23870195	GWAS catalog

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4820834	CABP7	cis	cerebellum	SCAN
rs4820834	PIK3IP1	cis	cerebellum	SCAN
rs4820834	RP1-130H16.16	cis	Thyroid	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:30748800-30752000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr22:30749000-30751800	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
3	chr22:30749000-30752000	Weak transcription	Aorta	Aorta
4	chr22:30749200-30752000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr22:30750000-30751800	Enhancers	Left Ventricle	heart
6	chr22:30750200-30751800	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
7	chr22:30750200-30751800	Genic enhancers	Placenta	Placenta
8	chr22:30750200-30752000	Enhancers	Gastric	stomach
9	chr22:30750200-30752000	Enhancers	Lung	lung
10	chr22:30750200-30752000	Enhancers	Pancreas	Pancrea
11	chr22:30750200-30752000	Enhancers	Small Intestine	intestine
12	chr22:30750400-30751800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
13	chr22:30750400-30751800	Enhancers	Stomach Mucosa	stomach
14	chr22:30750600-30751800	Enhancers	Primary monocytes fromperipheralblood	blood
15	chr22:30750600-30752200	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
16	chr22:30750600-30752600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
17	chr22:30750600-30754400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr22:30750800-30751800	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr22:30750800-30751800	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
20	chr22:30750800-30752000	Enhancers	Sigmoid Colon	Sigmoid Colon
21	chr22:30750800-30752000	Enhancers	Spleen	Spleen
22	chr22:30750800-30752200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
23	chr22:30750800-30752400	Flanking Active TSS	Primary B cells from cord blood	blood
24	chr22:30750800-30752400	Flanking Active TSS	Stomach Smooth Muscle	stomach
25	chr22:30751000-30751800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr22:30751000-30752000	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
27	chr22:30751000-30752000	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
28	chr22:30751000-30752000	Flanking Active TSS	Brain Anterior Caudate	brain
29	chr22:30751000-30752000	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
30	chr22:30751000-30752400	Flanking Active TSS	Primary T cells from cord blood	blood
31	chr22:30751000-30752400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr22:30751000-30752400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr22:30751200-30751800	Flanking Active TSS	Brain Hippocampus Middle	brain
34	chr22:30751200-30751800	Flanking Active TSS	Right Atrium	heart
35	chr22:30751200-30751800	Flanking Active TSS	GM12878-XiMat	blood
36	chr22:30751200-30751800	Flanking Active TSS	HMEC	breast
37	chr22:30751200-30752000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr22:30751200-30752000	Flanking Active TSS	Brain Germinal Matrix	brain
39	chr22:30751200-30752000	Enhancers	Placenta Amnion	Placenta Amnion
40	chr22:30751200-30752000	Flanking Active TSS	Hela-S3	cervix
41	chr22:30751200-30752000	Flanking Active TSS	NHLF	lung
42	chr22:30751200-30752200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr22:30751200-30752200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr22:30751200-30752200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
45	chr22:30751200-30752200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr22:30751200-30752200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr22:30751200-30752200	Flanking Active TSS	Fetal Heart	heart
48	chr22:30751200-30752200	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
49	chr22:30751200-30752200	Flanking Active TSS	NHEK	skin
50	chr22:30751200-30752200	Flanking Active TSS	Osteobl	bone

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