Variant report

Variant	rs5997637
Chromosome Location	chr22:30794950-30794951
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:16)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:16 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GATA1	chr22:30794816-30795324	PBDE	blood:	n/a	chr22:30795115-30795125
2	POLR2A	chr22:30793321-30795253	Raji	blood:	n/a	n/a
3	MAX	chr22:30794885-30795260	NB4	blood:	n/a	n/a
4	POLR2A	chr22:30794943-30795163	A549	lung:	n/a	n/a
5	POLR2A	chr22:30794232-30795083	Hela-S3	cervix:	n/a	n/a
6	POLR2A	chr22:30793524-30795326	PBDE	blood:	n/a	n/a
7	POLR2A	chr22:30791787-30796585	GM12878	blood:	n/a	n/a
8	POLR2A	chr22:30792617-30795297	GM12878	blood:	n/a	n/a
9	POLR2A	chr22:30792819-30795221	Hela-S3	cervix:	n/a	n/a
10	ZNF143	chr22:30794785-30794976	K562	blood:	n/a	n/a
11	POLR2A	chr22:30794846-30795316	HL-60	blood:	n/a	n/a
12	POLR2A	chr22:30793918-30795516	HepG2	liver:	n/a	n/a
13	POLR2A	chr22:30794473-30795298	GM12878	blood:	n/a	n/a
14	POLR2A	chr22:30794910-30795013	K562	blood:	n/a	n/a
15	POLR2A	chr22:30792640-30795327	K562	blood:	n/a	n/a
16	POLR2A	chr22:30794186-30794980	HepG2	liver:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr22:30787731..30797808-chr22:30813672..30825727,31	MCF-7	breast:
2	chr22:30793027..30795107-chr22:30817004..30819701,2	K562	blood:
3	chr17:56736502..56738510-chr22:30792727..30794981,2	MCF-7	breast:
4	chr22:30791754..30798377-chr22:30814746..30822334,13	K562	blood:

No data

Variant related genes	Relation type
SEC14L2	TF binding region
ENSG00000222915	Chromatin interaction
ENSG00000242114	Chromatin interaction
ENSG00000273350	Chromatin interaction
ENSG00000272689	Chromatin interaction
ENSG00000099999	Chromatin interaction
ENSG00000202077	Chromatin interaction
ENSG00000268538	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs1005835	0.84[CEU][hapmap];0.85[JPT][hapmap];0.87[EUR][1000 genomes]
rs1010324	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11089442	0.82[CEU][hapmap];0.83[MEX][hapmap]
rs11089447	0.92[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];0.85[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs11089448	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11089449	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11703867	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11705639	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12171261	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2072160	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2074731	0.91[CEU][hapmap];0.91[MEX][hapmap];0.84[TSI][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2267154	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2267155	1.00[CEU][hapmap];0.91[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2267156	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.94[TSI][hapmap];0.96[YRI][hapmap];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2283866	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2283870	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2283871	0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2299827	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]
rs2839998	0.91[CEU][hapmap];0.91[MEX][hapmap];0.84[TSI][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs57940170	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs5994294	0.91[CEU][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs5994305	0.92[ASW][hapmap];1.00[CEU][hapmap];0.98[GIH][hapmap];0.90[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs5994306	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs5997646	1.00[CEU][hapmap];0.90[JPT][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.83[YRI][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs61583714	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs71331235	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7288366	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]
rs7289360	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7290317	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8141656	0.91[CEU][hapmap];0.91[MEX][hapmap];0.84[TSI][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9619096	0.91[CEU][hapmap];0.91[MEX][hapmap];0.84[TSI][hapmap];0.80[EUR][1000 genomes]
rs9619098	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9619105	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9620984	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[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
rs5997637	NIPSNAP1	cis	parietal	SCAN
rs5997637	SYN3	cis	parietal	SCAN

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:30792600-30795400	Enhancers	Spleen	Spleen
2	chr22:30792800-30795000	Active TSS	Breast Myoepithelial Primary Cells	Breast
3	chr22:30792800-30795600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr22:30793400-30795000	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
5	chr22:30793400-30795200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
6	chr22:30793400-30795400	Flanking Active TSS	Dnd41	blood
7	chr22:30793600-30795000	Flanking Active TSS	Primary T cells from cord blood	blood
8	chr22:30793600-30795000	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
9	chr22:30793600-30795000	Flanking Active TSS	Brain Hippocampus Middle	brain
10	chr22:30793600-30795000	Flanking Active TSS	Brain Substantia Nigra	brain
11	chr22:30793600-30795000	Flanking Active TSS	Osteobl	bone
12	chr22:30793600-30795200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr22:30793600-30795200	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
14	chr22:30793600-30795200	Enhancers	K562	blood
15	chr22:30793600-30795200	Flanking Active TSS	NH-A	brain
16	chr22:30793600-30795400	Flanking Active TSS	Liver	Liver
17	chr22:30793600-30795400	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
18	chr22:30793800-30795200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
19	chr22:30793800-30795200	Enhancers	Pancreas	Pancrea
20	chr22:30793800-30795400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr22:30794000-30795000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
22	chr22:30794000-30795000	Enhancers	Primary T killer memory cells from peripheral blood	blood
23	chr22:30794000-30795000	Bivalent Enhancer	Primary mononuclear cells fromperipheralblood	Blood
24	chr22:30794000-30795000	Bivalent Enhancer	Adipose Nuclei	Adipose
25	chr22:30794000-30795000	Enhancers	Fetal Lung	lung
26	chr22:30794000-30795200	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
27	chr22:30794000-30795200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr22:30794000-30795200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr22:30794000-30795200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr22:30794000-30795200	Flanking Active TSS	Brain Cingulate Gyrus	brain
31	chr22:30794000-30795200	Enhancers	Ovary	ovary
32	chr22:30794000-30795200	Bivalent Enhancer	Skeletal Muscle Female	skeletal muscle
33	chr22:30794000-30795200	Enhancers	Small Intestine	intestine
34	chr22:30794000-30816600	Weak transcription	Pancreatic Islets	Pancreatic Islet
35	chr22:30794000-30818000	Weak transcription	Right Atrium	heart
36	chr22:30794200-30795000	Bivalent Enhancer	Colonic Mucosa	Colon
37	chr22:30794200-30795000	Flanking Active TSS	NHLF	lung
38	chr22:30794200-30795200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr22:30794200-30795200	Flanking Active TSS	Brain Angular Gyrus	brain
40	chr22:30794200-30795200	Flanking Active TSS	NHEK	skin
41	chr22:30794200-30795800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr22:30794200-30796200	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr22:30794200-30797800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr22:30794200-30797800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr22:30794400-30795000	Enhancers	Colon Smooth Muscle	Colon
46	chr22:30794400-30795000	Enhancers	Fetal Intestine Small	intestine
47	chr22:30794400-30795200	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
48	chr22:30794400-30795200	Bivalent Enhancer	Primary hematopoietic stem cells short term culture	blood
49	chr22:30794400-30795200	Enhancers	Fetal Intestine Large	intestine
50	chr22:30794400-30795200	Flanking Active TSS	HMEC	breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links