Variant report

Variant	rs7628406
Chromosome Location	chr3:53318493-53318494
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:53317678-53318533	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:53317349..53318958-chr3:53320519..53322131,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TKT-1	chr3:53317449-53319252	NONHSAT089991

Variant related genes	Relation type
RN7SL821P	TF binding region
ENSG00000238565	TF binding region

Extended variants
information (count: 4 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs12496449	0.87[AFR][1000 genomes]
rs7626998	0.87[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv834699	chr3:53151876-53325808	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv517233	chr3:53175557-53321002	Transcr. at gene 5' and 3' Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:53304600-53318600	Weak transcription	Gastric	stomach
2	chr3:53304600-53320600	Weak transcription	Brain Angular Gyrus	brain
3	chr3:53304600-53325600	Weak transcription	Fetal Heart	heart
4	chr3:53304600-53326200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr3:53304800-53319000	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr3:53304800-53319400	Weak transcription	HSMM	muscle
7	chr3:53305000-53318600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr3:53305000-53318800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr3:53305000-53318800	Weak transcription	NHDF-Ad	bronchial
10	chr3:53305000-53319000	Weak transcription	Esophagus	oesophagus
11	chr3:53305000-53320200	Weak transcription	Colon Smooth Muscle	Colon
12	chr3:53305000-53324400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr3:53305400-53318800	Weak transcription	Duodenum Smooth Muscle	Duodenum
14	chr3:53305400-53319200	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr3:53305600-53318800	Weak transcription	Brain Cingulate Gyrus	brain
16	chr3:53305600-53319000	Weak transcription	HMEC	breast
17	chr3:53305600-53319800	Weak transcription	Brain Hippocampus Middle	brain
18	chr3:53305600-53320200	Weak transcription	Brain Substantia Nigra	brain
19	chr3:53309400-53320200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
20	chr3:53309400-53351200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr3:53309600-53320400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr3:53309800-53318800	Weak transcription	HUES64 Cell Line	embryonic stem cell
23	chr3:53309800-53318800	Weak transcription	Primary T helper cells PMA-I stimulated	--
24	chr3:53309800-53325600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
25	chr3:53309800-53326200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
26	chr3:53310200-53318600	Weak transcription	Fetal Lung	lung
27	chr3:53312200-53337400	Weak transcription	Psoas Muscle	Psoas
28	chr3:53312400-53328000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr3:53313200-53318800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
30	chr3:53313200-53319200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
31	chr3:53313200-53319200	Weak transcription	Fetal Brain Male	brain
32	chr3:53313200-53320600	Weak transcription	H9 Cell Line	embryonic stem cell
33	chr3:53313200-53321400	Weak transcription	Fetal Kidney	kidney
34	chr3:53314000-53318600	Weak transcription	Rectal Smooth Muscle	rectum
35	chr3:53314200-53318800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
36	chr3:53314200-53325600	Weak transcription	Colonic Mucosa	Colon
37	chr3:53314200-53326400	Weak transcription	K562	blood
38	chr3:53314600-53318600	Weak transcription	Rectal Mucosa Donor 31	rectum
39	chr3:53314800-53320600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr3:53315000-53320200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr3:53315200-53319200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
42	chr3:53315200-53320800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr3:53315200-53326800	Strong transcription	Primary B cells from cord blood	blood
44	chr3:53315200-53333800	Strong transcription	Primary monocytes fromperipheralblood	blood
45	chr3:53315200-53338400	Strong transcription	Fetal Muscle Trunk	muscle
46	chr3:53315400-53320400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr3:53315400-53320800	Strong transcription	Fetal Thymus	thymus
48	chr3:53315600-53319000	Weak transcription	Brain Germinal Matrix	brain
49	chr3:53315600-53322800	Strong transcription	Thymus	Thymus
50	chr3:53316000-53319000	Weak transcription	A549	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links