Variant report

Variant	rs5997638
Chromosome Location	chr22:30795011-30795012
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:15)
CpG islands
(count:0)
Chromatin interactive
region (count:3)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:15 , 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	POLR2A	chr22:30794846-30795316	HL-60	blood:	n/a	n/a
11	TAL1	chr22:30794969-30795115	K562	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

No data

(count:3 , 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	chr22:30791754..30798377-chr22:30814746..30822334,13	K562	blood:

No data

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

Extended variants
information (count: 5 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs12159316	0.89[AFR][1000 genomes]
rs5997618	0.89[AFR][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

No data

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	chr22:30792800-30795600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr22:30793400-30795200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
4	chr22:30793400-30795400	Flanking Active TSS	Dnd41	blood
5	chr22:30793600-30795200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr22:30793600-30795200	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
7	chr22:30793600-30795200	Enhancers	K562	blood
8	chr22:30793600-30795200	Flanking Active TSS	NH-A	brain
9	chr22:30793600-30795400	Flanking Active TSS	Liver	Liver
10	chr22:30793600-30795400	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
11	chr22:30793800-30795200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
12	chr22:30793800-30795200	Enhancers	Pancreas	Pancrea
13	chr22:30793800-30795400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr22:30794000-30795200	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
15	chr22:30794000-30795200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr22:30794000-30795200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr22:30794000-30795200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr22:30794000-30795200	Flanking Active TSS	Brain Cingulate Gyrus	brain
19	chr22:30794000-30795200	Enhancers	Ovary	ovary
20	chr22:30794000-30795200	Bivalent Enhancer	Skeletal Muscle Female	skeletal muscle
21	chr22:30794000-30795200	Enhancers	Small Intestine	intestine
22	chr22:30794000-30816600	Weak transcription	Pancreatic Islets	Pancreatic Islet
23	chr22:30794000-30818000	Weak transcription	Right Atrium	heart
24	chr22:30794200-30795200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr22:30794200-30795200	Flanking Active TSS	Brain Angular Gyrus	brain
26	chr22:30794200-30795200	Flanking Active TSS	NHEK	skin
27	chr22:30794200-30795800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr22:30794200-30796200	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr22:30794200-30797800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr22:30794200-30797800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr22:30794400-30795200	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
32	chr22:30794400-30795200	Bivalent Enhancer	Primary hematopoietic stem cells short term culture	blood
33	chr22:30794400-30795200	Enhancers	Fetal Intestine Large	intestine
34	chr22:30794400-30795200	Flanking Active TSS	HMEC	breast
35	chr22:30794400-30795200	Enhancers	NHDF-Ad	bronchial
36	chr22:30794400-30802200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr22:30794400-30811800	Weak transcription	H9 Cell Line	embryonic stem cell
38	chr22:30794600-30795200	Transcr. at gene 5' and 3'	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr22:30794600-30795200	Enhancers	Fetal Brain Female	brain
40	chr22:30794600-30795200	Enhancers	Gastric	stomach
41	chr22:30794600-30795200	Enhancers	Stomach Mucosa	stomach
42	chr22:30794600-30795200	Transcr. at gene 5' and 3'	HSMM	muscle
43	chr22:30794600-30795400	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
44	chr22:30794600-30795400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
45	chr22:30794600-30795400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
46	chr22:30794600-30796200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr22:30794600-30796400	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr22:30794600-30798000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr22:30794600-30798000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
50	chr22:30794600-30802200	Weak transcription	Aorta	Aorta

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links