Variant report

Variant	rs72969253
Chromosome Location	chr4:106626074-106626075
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:2 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr4:106625753-106626360	K562	blood:	n/a	n/a
2	POLR2A	chr4:106625746-106626513	GM12878	blood:	n/a	n/a

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr4:106622664..106627326-chr4:106627806..106630924,8	MCF-7	breast:
2	chr4:106621555..106624339-chr4:106624780..106626817,2	K562	blood:
3	chr4:106625552..106627998-chr4:106628396..106630043,4	MCF-7	breast:
4	chr4:106625477..106627782-chr4:106631303..106633402,2	K562	blood:
5	chr4:106625302..106627782-chr4:106631303..106633402,3	K562	blood:
6	chr4:106625095..106627707-chr4:106631169..106633895,2	MCF-7	breast:
7	chr4:106610718..106612290-chr4:106624783..106626810,2	MCF-7	breast:
8	chr4:106609114..106611557-chr4:106624623..106627601,2	K562	blood:
9	chr4:106623594..106626917-chr4:106627781..106630373,5	K562	blood:
10	chr4:106616699..106623307-chr4:106623731..106631342,11	K562	blood:

No data

Variant related genes	Relation type
GSTCD	TF binding region
ENSG00000138780	Chromatin interaction
ENSG00000138785	Chromatin interaction
ENSG00000236699	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs17036260	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56924509	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57357762	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6812579	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6827293	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6832006	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6841297	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6842870	0.83[AFR][1000 genomes]
rs6850604	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs72956940	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72960918	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72960924	0.83[AFR][1000 genomes]
rs72969249	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72969275	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7666495	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7671981	0.98[AFR][1000 genomes]
rs7691960	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv879699	chr4:106212562-106698892	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:106587800-106629000	Weak transcription	Lung	lung
2	chr4:106600400-106628600	Weak transcription	Colonic Mucosa	Colon
3	chr4:106600600-106628400	Weak transcription	Stomach Mucosa	stomach
4	chr4:106601200-106628400	Weak transcription	Psoas Muscle	Psoas
5	chr4:106602200-106629200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr4:106602400-106628600	Weak transcription	Right Ventricle	heart
7	chr4:106602600-106628400	Weak transcription	Fetal Heart	heart
8	chr4:106602600-106629200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr4:106604400-106629200	Weak transcription	Esophagus	oesophagus
10	chr4:106604400-106629200	Weak transcription	Gastric	stomach
11	chr4:106606600-106628200	Weak transcription	Hela-S3	cervix
12	chr4:106607600-106626400	Weak transcription	Small Intestine	intestine
13	chr4:106610400-106628800	Weak transcription	Fetal Kidney	kidney
14	chr4:106610600-106628200	Weak transcription	Fetal Brain Male	brain
15	chr4:106610600-106628600	Weak transcription	A549	lung
16	chr4:106610800-106628600	Weak transcription	Brain Cingulate Gyrus	brain
17	chr4:106611400-106627600	Weak transcription	HepG2	liver
18	chr4:106611400-106628600	Weak transcription	Skeletal Muscle Male	skeletal muscle
19	chr4:106613600-106628600	Weak transcription	Aorta	Aorta
20	chr4:106613600-106628600	Weak transcription	Ovary	ovary
21	chr4:106614600-106628400	Weak transcription	Rectal Smooth Muscle	rectum
22	chr4:106614800-106628200	Weak transcription	Brain Angular Gyrus	brain
23	chr4:106615000-106628600	Weak transcription	Colon Smooth Muscle	Colon
24	chr4:106615800-106628600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
25	chr4:106615800-106628600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr4:106616000-106628400	Weak transcription	NHLF	lung
27	chr4:106616000-106628600	Weak transcription	HUES64 Cell Line	embryonic stem cell
28	chr4:106616000-106629000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr4:106616200-106628400	Weak transcription	Brain Germinal Matrix	brain
30	chr4:106616400-106628400	Weak transcription	Thymus	Thymus
31	chr4:106616400-106628600	Weak transcription	Rectal Mucosa Donor 31	rectum
32	chr4:106616800-106628600	Weak transcription	HUES48 Cell Line	embryonic stem cell
33	chr4:106616800-106628600	Weak transcription	NH-A	brain
34	chr4:106617400-106627600	Weak transcription	Fetal Intestine Small	intestine
35	chr4:106617400-106628600	Weak transcription	Fetal Intestine Large	intestine
36	chr4:106617400-106628800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr4:106617400-106629000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr4:106617400-106629000	Weak transcription	Pancreas	Pancrea
39	chr4:106617600-106626200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
40	chr4:106617600-106628000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
41	chr4:106617600-106628400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
42	chr4:106617600-106628400	Weak transcription	Brain Inferior Temporal Lobe	brain
43	chr4:106618200-106626400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr4:106619200-106628600	Weak transcription	Fetal Stomach	stomach
45	chr4:106619200-106629000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
46	chr4:106619400-106628600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
47	chr4:106619400-106628600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr4:106619400-106628600	Weak transcription	Stomach Smooth Muscle	stomach
49	chr4:106619600-106626200	Weak transcription	Fetal Lung	lung
50	chr4:106620000-106628200	Weak transcription	Brain Hippocampus Middle	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links