Variant report

Variant	rs3769297
Chromosome Location	chr2:173724086-173724087
allele	G/T
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	MXI1	chr2:173722921-173728161	SK-N-SH	brain:	n/a	n/a

Variant related genes	Relation type
RAPGEF4	TF binding region

Extended variants
information (count: 8 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs12478288	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12612612	0.93[EUR][1000 genomes]
rs12618968	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12622141	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17706463	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3769289	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3769295	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][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	nsv533927	chr2:173161637-173796894	Active TSS Enhancers Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:173719800-173724400	Weak transcription	Brain Cingulate Gyrus	brain
2	chr2:173721600-173726000	Weak transcription	Gastric	stomach
3	chr2:173722000-173724200	Weak transcription	Fetal Intestine Small	intestine
4	chr2:173722000-173724400	Weak transcription	Fetal Intestine Large	intestine
5	chr2:173722200-173724800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
6	chr2:173722200-173727400	Enhancers	Fetal Heart	heart
7	chr2:173722800-173724200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr2:173722800-173724400	Enhancers	HUVEC	blood vessel
9	chr2:173723000-173724400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr2:173723000-173725200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr2:173723200-173724200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr2:173723400-173724400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr2:173723400-173724400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr2:173723400-173724400	Enhancers	Pancreatic Islets	Pancreatic Islet
15	chr2:173723400-173724400	Weak transcription	Fetal Stomach	stomach
16	chr2:173723400-173724400	Weak transcription	Small Intestine	intestine
17	chr2:173723400-173724400	Weak transcription	HMEC	breast
18	chr2:173723400-173724400	Enhancers	NHEK	skin
19	chr2:173723400-173724600	Weak transcription	Left Ventricle	heart
20	chr2:173723400-173724600	Weak transcription	Right Ventricle	heart
21	chr2:173723400-173724800	Weak transcription	NH-A	brain
22	chr2:173723400-173728800	Weak transcription	Pancreas	Pancrea
23	chr2:173723600-173724800	Weak transcription	Fetal Lung	lung
24	chr2:173723800-173724200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr2:173723800-173724200	Weak transcription	Cortex derived primary cultured neurospheres	brain
26	chr2:173723800-173724600	Enhancers	Duodenum Mucosa	Duodenum
27	chr2:173724000-173724200	Enhancers	Brain Anterior Caudate	brain
28	chr2:173724000-173724200	Enhancers	Rectal Smooth Muscle	rectum
29	chr2:173724000-173724400	Flanking Active TSS	Hela-S3	cervix
30	chr2:173724000-173725000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links