Variant report

Variant	rs7288366
Chromosome Location	chr22:30796422-30796423
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr22:30787731..30797808-chr22:30813672..30825727,31	MCF-7	breast:
2	chr22:30791627..30794347-chr22:30796334..30798708,2	MCF-7	breast:
3	chr22:30791631..30793562-chr22:30796182..30798580,3	K562	blood:
4	chr22:30791754..30798377-chr22:30814746..30822334,13	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RP4-539M6.19.1-2	chr22:30796248-30796456	NONHSAT084779

Variant related genes	Relation type
ENSG00000272689	Chromatin interaction
ENSG00000268538	Chromatin interaction
ENSG00000273350	Chromatin interaction
ENSG00000099999	Chromatin interaction
ENSG00000242114	Chromatin interaction
ENSG00000222915	Chromatin interaction
ENSG00000100003	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs1005835	0.84[CEU][hapmap];0.85[JPT][hapmap];0.87[EUR][1000 genomes]
rs1010324	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11089442	0.82[CEU][hapmap];0.83[MEX][hapmap];0.81[TSI][hapmap]
rs11089447	0.85[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.91[TSI][hapmap];0.81[YRI][hapmap];0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11089448	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11089449	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11703385	0.81[EUR][1000 genomes]
rs11703867	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11705639	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12171261	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2072160	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2074731	0.91[CEU][hapmap];0.82[GIH][hapmap];0.91[MEX][hapmap];0.90[TSI][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2267154	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2267155	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2267156	0.92[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2283866	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2283870	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2283871	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2299827	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]
rs2839998	0.91[CEU][hapmap];0.84[GIH][hapmap];0.91[MEX][hapmap];0.90[TSI][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs57940170	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs5994294	0.91[CEU][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs5994305	0.85[ASW][hapmap];1.00[CEU][hapmap];0.81[CHB][hapmap];0.91[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs5994306	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs5997637	0.92[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.81[YRI][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs5997646	1.00[CEU][hapmap];0.90[JPT][hapmap];0.91[MEX][hapmap];0.90[TSI][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs61583714	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs71331235	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7289360	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7290317	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8141656	0.91[CEU][hapmap];0.84[GIH][hapmap];0.91[MEX][hapmap];0.90[TSI][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9619096	0.91[CEU][hapmap];0.91[MEX][hapmap];0.90[TSI][hapmap];0.83[EUR][1000 genomes]
rs9619098	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9619105	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9620984	1.00[CEU][hapmap];0.90[CHB][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7288366	NIPSNAP1	cis	parietal	SCAN
rs7288366	SYN3	cis	parietal	SCAN

Chromatin state (count:90 , 50 per page) page: 1 2

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	chr22:30794200-30797800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr22:30794200-30797800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr22:30794400-30802200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr22:30794400-30811800	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr22:30794600-30798000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr22:30794600-30798000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr22:30794600-30802200	Weak transcription	Aorta	Aorta
10	chr22:30794600-30803200	Weak transcription	Fetal Brain Male	brain
11	chr22:30794600-30803200	Weak transcription	Lung	lung
12	chr22:30794600-30811400	Weak transcription	Right Ventricle	heart
13	chr22:30794800-30796600	Genic enhancers	Cortex derived primary cultured neurospheres	brain
14	chr22:30794800-30796600	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr22:30794800-30796600	Enhancers	Fetal Thymus	thymus
16	chr22:30794800-30797800	Weak transcription	A549	lung
17	chr22:30794800-30798000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
18	chr22:30794800-30802800	Weak transcription	Hela-S3	cervix
19	chr22:30794800-30811400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
20	chr22:30794800-30811600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr22:30794800-30818600	Weak transcription	Primary B cells from cord blood	blood
22	chr22:30795000-30802600	Weak transcription	Fetal Lung	lung
23	chr22:30795000-30809800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
24	chr22:30795000-30814600	Weak transcription	Colon Smooth Muscle	Colon
25	chr22:30795200-30796600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr22:30795200-30797800	Weak transcription	Brain Angular Gyrus	brain
27	chr22:30795200-30797800	Weak transcription	Fetal Intestine Large	intestine
28	chr22:30795200-30797800	Weak transcription	Ovary	ovary
29	chr22:30795200-30797800	Weak transcription	Stomach Mucosa	stomach
30	chr22:30795200-30797800	Weak transcription	Osteobl	bone
31	chr22:30795200-30798000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr22:30795200-30798000	Weak transcription	K562	blood
33	chr22:30795200-30798200	Weak transcription	HUVEC	blood vessel
34	chr22:30795200-30799200	Weak transcription	Duodenum Mucosa	Duodenum
35	chr22:30795200-30799200	Strong transcription	Fetal Intestine Small	intestine
36	chr22:30795200-30799400	Weak transcription	Thymus	Thymus
37	chr22:30795200-30801200	Weak transcription	Gastric	stomach
38	chr22:30795200-30801400	Weak transcription	Primary T cells from cord blood	blood
39	chr22:30795200-30801800	Weak transcription	Primary T helper cells fromperipheralblood	blood
40	chr22:30795200-30802200	Weak transcription	Fetal Brain Female	brain
41	chr22:30795200-30803000	Weak transcription	Rectal Smooth Muscle	rectum
42	chr22:30795200-30804600	Weak transcription	NHDF-Ad	bronchial
43	chr22:30795200-30804800	Weak transcription	Pancreas	Pancrea
44	chr22:30795200-30807800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
45	chr22:30795200-30809000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
46	chr22:30795200-30810200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
47	chr22:30795200-30811600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
48	chr22:30795200-30814400	Weak transcription	Small Intestine	intestine
49	chr22:30795400-30797800	Weak transcription	NH-A	brain
50	chr22:30795400-30802200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood

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