Variant report

Variant	rs2299829
Chromosome Location	chr22:30817370-30817371
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:9)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:9 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GATA1	chr22:30816326-30818234	PBDE	blood:	n/a	n/a
2	POLR2A	chr22:30816171-30817395	HUVEC	blood vessel:	n/a	n/a
3	POLR2A	chr22:30816349-30821249	IMR90	lung:	n/a	n/a
4	CHD1	chr22:30816159-30822993	IMR90	lung:	n/a	n/a
5	POLR2A	chr22:30816245-30822974	PBDE	blood:	n/a	n/a
6	POLR2A	chr22:30817129-30818359	HUVEC	blood vessel:	n/a	n/a
7	POLR2A	chr22:30817301-30817400	MCF10A-Er-Src	breast:	n/a	n/a
8	RCOR1	chr22:30816050-30822994	IMR90	lung:	n/a	n/a
9	IRF1	chr22:30816790-30818424	K562	blood:	n/a	chr22:30816935-30816945 chr22:30816802-30816822 chr22:30816931-30816945 chr22:30816933-30816947

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr22:30814763..30819112-chr22:30819393..30823307,5	MCF-7	breast:
2	chr22:30816361..30822733-chr22:30829064..30833429,8	K562	blood:
3	chr22:30812731..30815358-chr22:30815799..30818479,2	MCF-7	breast:
4	chr22:30793027..30795107-chr22:30817004..30819701,2	K562	blood:
5	chr22:30641395..30644994-chr22:30815782..30819866,5	MCF-7	breast:
6	chr22:30791754..30798377-chr22:30814746..30822334,13	K562	blood:
7	chr22:30801331..30806439-chr22:30816907..30821751,5	K562	blood:
8	chr22:30780386..30782265-chr22:30815840..30818586,2	MCF-7	breast:
9	chr22:30787731..30797808-chr22:30813672..30825727,31	MCF-7	breast:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SEC14L3-2	chr22:30817195-30817525	ENSG00000272689.1

No data

Variant related genes	Relation type
ENSG00000268538	TF binding region
MTFP1	TF binding region
ENSG00000242114	Chromatin interaction
ENSG00000100003	Chromatin interaction
ENSG00000099999	Chromatin interaction
ENSG00000203606	Chromatin interaction
ENSG00000268538	Chromatin interaction
ENSG00000249590	Chromatin interaction
ENSG00000128342	Chromatin interaction
ENSG00000268812	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs17658686	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2299824	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2412985	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4820011	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4820845	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7292432	0.86[AMR][1000 genomes];0.86[EUR][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:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:30794000-30818000	Weak transcription	Right Atrium	heart
2	chr22:30794800-30818600	Weak transcription	Primary B cells from cord blood	blood
3	chr22:30799400-30817600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr22:30805000-30818200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr22:30808400-30817400	Strong transcription	Fetal Muscle Leg	muscle
6	chr22:30809000-30818200	Strong transcription	Fetal Brain Female	brain
7	chr22:30809800-30818400	Weak transcription	Primary monocytes fromperipheralblood	blood
8	chr22:30809800-30818400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr22:30810000-30817800	Strong transcription	HUES64 Cell Line	embryonic stem cell
10	chr22:30810600-30817800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
11	chr22:30811000-30818000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
12	chr22:30811400-30817600	Strong transcription	Skeletal Muscle Male	skeletal muscle
13	chr22:30811800-30818200	Strong transcription	Primary T cells from cord blood	blood
14	chr22:30812400-30818200	Weak transcription	Primary hematopoietic stem cells	blood
15	chr22:30812600-30817800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr22:30812600-30818800	Weak transcription	Primary neutrophils fromperipheralblood	blood
17	chr22:30812800-30817600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr22:30812800-30818000	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr22:30812800-30818200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr22:30812800-30818400	Weak transcription	Fetal Brain Male	brain
21	chr22:30813000-30817800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr22:30813400-30818400	Genic enhancers	HMEC	breast
23	chr22:30813800-30817800	Weak transcription	H1 Cell Line	embryonic stem cell
24	chr22:30813800-30817800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
25	chr22:30814000-30817600	Weak transcription	Right Ventricle	heart
26	chr22:30814000-30818800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr22:30814200-30817400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
28	chr22:30814400-30817400	Strong transcription	Primary B cells from peripheral blood	blood
29	chr22:30814600-30817800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr22:30814600-30818600	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr22:30814600-30818600	Enhancers	Fetal Intestine Large	intestine
32	chr22:30814800-30817800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
33	chr22:30814800-30818200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr22:30814800-30819000	Weak transcription	Aorta	Aorta
35	chr22:30815000-30817800	Weak transcription	Left Ventricle	heart
36	chr22:30815000-30818400	Weak transcription	Monocytes-CD14+_RO01746	blood
37	chr22:30815200-30817400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr22:30815200-30817800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
39	chr22:30815200-30818000	Weak transcription	Colon Smooth Muscle	Colon
40	chr22:30815200-30818000	Weak transcription	Esophagus	oesophagus
41	chr22:30815200-30818000	Weak transcription	Fetal Lung	lung
42	chr22:30815200-30818200	Weak transcription	Adipose Nuclei	Adipose
43	chr22:30815200-30818400	Weak transcription	Thymus	Thymus
44	chr22:30815200-30818600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
45	chr22:30815200-30818600	Weak transcription	Fetal Kidney	kidney
46	chr22:30815200-30818600	Genic enhancers	NHEK	skin
47	chr22:30815400-30818000	Weak transcription	Pancreas	Pancrea
48	chr22:30815400-30818200	Weak transcription	Spleen	Spleen
49	chr22:30815600-30818000	Weak transcription	Primary T helper cells fromperipheralblood	blood
50	chr22:30815800-30818400	Genic enhancers	HSMM	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links