Variant report

Variant	rs2299827
Chromosome Location	chr22:30814727-30814728
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:7)
CpG islands
(count:0)
Chromatin interactive
region (count:3)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:7 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOXA1	chr22:30814682-30815329	HepG2	liver:	n/a	n/a
2	FOXA1	chr22:30814675-30815334	HepG2	liver:	n/a	n/a
3	FOXA1	chr22:30814680-30815260	HepG2	liver:	n/a	n/a
4	NFIC	chr22:30814710-30815315	HepG2	liver:	n/a	n/a
5	FOSL2	chr22:30814724-30815226	HepG2	liver:	n/a	n/a
6	MYBL2	chr22:30814667-30815352	HepG2	liver:	n/a	n/a
7	EP300	chr22:30814716-30815240	HepG2	liver:	n/a	n/a

No data

(count:3 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr22:30812731..30815358-chr22:30815799..30818479,2	MCF-7	breast:
2	chr22:30787731..30797808-chr22:30813672..30825727,31	MCF-7	breast:
3	chr22:30802321..30807877-chr22:30810760..30815440,6	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000268538	TF binding region
RNU6-564P	TF binding region
ENSG00000273350	TF binding region
ENSG00000222915	Chromatin interaction
ENSG00000273350	Chromatin interaction
ENSG00000100003	Chromatin interaction
ENSG00000272689	Chromatin interaction
ENSG00000099999	Chromatin interaction
ENSG00000249590	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs1005835	0.85[JPT][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1010324	0.91[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11089442	0.81[CHB][hapmap];0.81[TSI][hapmap]
rs11089447	0.92[ASW][hapmap];0.91[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];0.91[TSI][hapmap];0.96[YRI][hapmap];0.91[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs11089448	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11089449	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11703867	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11705639	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12171261	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2072160	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2074731	0.83[CEU][hapmap];0.82[GIH][hapmap];0.87[MEX][hapmap];0.90[TSI][hapmap];0.82[EUR][1000 genomes]
rs2267154	0.91[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2267155	0.91[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.94[TSI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2267156	1.00[ASW][hapmap];0.91[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2283866	0.81[EUR][1000 genomes]
rs2283870	0.91[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2283871	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2839998	0.83[CEU][hapmap];0.81[CHB][hapmap];0.84[GIH][hapmap];0.87[MEX][hapmap];0.90[TSI][hapmap];0.83[EUR][1000 genomes]
rs57940170	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs5994294	0.83[CEU][hapmap];0.81[CHB][hapmap];0.82[EUR][1000 genomes]
rs5994305	0.92[ASW][hapmap];0.91[CEU][hapmap];0.91[GIH][hapmap];0.90[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs5994306	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs5997637	1.00[ASW][hapmap];0.91[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];0.96[YRI][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs5997646	0.91[CEU][hapmap];0.90[JPT][hapmap];0.87[MEX][hapmap];0.90[TSI][hapmap];0.88[YRI][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs61583714	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs71331235	0.82[EUR][1000 genomes]
rs7288366	0.92[ASW][hapmap];0.91[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7289360	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7290317	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8141656	0.83[CEU][hapmap];0.81[CHB][hapmap];0.84[GIH][hapmap];0.87[MEX][hapmap];0.90[TSI][hapmap];0.82[EUR][1000 genomes]
rs9619096	0.83[CEU][hapmap];0.81[CHB][hapmap];0.87[MEX][hapmap];0.90[TSI][hapmap]
rs9619098	0.82[EUR][1000 genomes]
rs9619105	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9620984	0.91[CEU][hapmap];1.00[CHB][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.94[TSI][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][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	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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2299827	NIPSNAP1	cis	parietal	SCAN
rs2299827	SYN3	cis	parietal	SCAN
rs2299827	TTC28AS	cis	parietal	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:30794000-30816600	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr22:30794000-30818000	Weak transcription	Right Atrium	heart
3	chr22:30794800-30818600	Weak transcription	Primary B cells from cord blood	blood
4	chr22:30797800-30816400	Strong transcription	Dnd41	blood
5	chr22:30799400-30817600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr22:30801400-30816600	Strong transcription	Fetal Stomach	stomach
7	chr22:30802000-30816400	Strong transcription	Stomach Smooth Muscle	stomach
8	chr22:30802200-30816200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr22:30802200-30817000	Genic enhancers	Liver	Liver
10	chr22:30802600-30814800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr22:30803200-30817200	Strong transcription	Fetal Muscle Trunk	muscle
12	chr22:30803400-30815200	Strong transcription	Brain Substantia Nigra	brain
13	chr22:30804800-30815600	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
14	chr22:30805000-30818200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr22:30805200-30816400	Weak transcription	NHDF-Ad	bronchial
16	chr22:30805800-30816200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr22:30805800-30816200	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr22:30806600-30815600	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr22:30807000-30816200	Strong transcription	Brain Hippocampus Middle	brain
20	chr22:30808400-30815200	Strong transcription	Thymus	Thymus
21	chr22:30808400-30817400	Strong transcription	Fetal Muscle Leg	muscle
22	chr22:30808800-30815200	Strong transcription	NH-A	brain
23	chr22:30809000-30815200	Strong transcription	Fetal Lung	lung
24	chr22:30809000-30815200	Strong transcription	NHLF	lung
25	chr22:30809000-30818200	Strong transcription	Fetal Brain Female	brain
26	chr22:30809800-30818400	Weak transcription	Primary monocytes fromperipheralblood	blood
27	chr22:30809800-30818400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
28	chr22:30810000-30817800	Strong transcription	HUES64 Cell Line	embryonic stem cell
29	chr22:30810200-30815600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr22:30810400-30816400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr22:30810600-30815400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
32	chr22:30810600-30817800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
33	chr22:30810800-30815000	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
34	chr22:30810800-30815200	Strong transcription	HUES6 Cell Line	embryonic stem cell
35	chr22:30810800-30815400	Strong transcription	Skeletal Muscle Female	skeletal muscle
36	chr22:30810800-30815800	Strong transcription	HSMM	muscle
37	chr22:30810800-30816400	Weak transcription	Fetal Heart	heart
38	chr22:30811000-30814800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr22:30811000-30815400	Strong transcription	Brain Angular Gyrus	brain
40	chr22:30811000-30818000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
41	chr22:30811200-30817000	Strong transcription	Rectal Mucosa Donor 29	rectum
42	chr22:30811400-30815000	Strong transcription	HUES48 Cell Line	embryonic stem cell
43	chr22:30811400-30815000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
44	chr22:30811400-30815000	Strong transcription	Left Ventricle	heart
45	chr22:30811400-30815200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr22:30811400-30815200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr22:30811400-30815200	Strong transcription	Adipose Nuclei	Adipose
48	chr22:30811400-30815200	Strong transcription	Placenta	Placenta
49	chr22:30811400-30815200	Strong transcription	HSMMtube	muscle
50	chr22:30811400-30815400	Strong transcription	Primary hematopoietic stem cells short term culture	blood

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