Variant report

Variant	rs173969
Chromosome Location	chr5:40841956-40841957
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:116184240..116184758-chr5:40841642..40842505,2	Hela-S3	cervix:

Variant related genes	Relation type
ENSG00000173218	Chromatin interaction

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

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

rs_ID	r²[population]
rs6887174	0.85[CHB][hapmap]
rs7715597	0.84[GIH][hapmap]

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	nsv880438	chr5:40753877-40900717	Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	160 gene(s)	inside rSNPs	diseases
2	nsv597877	chr5:40796746-40848803	Genic enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	158 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs173969	FGF10	cis	parietal	SCAN
rs173969	NUP155	cis	parietal	SCAN
rs173969	DAB2	cis	cerebellum	SCAN
rs173969	RPL37	cis	cerebellum	SCAN

Chromatin state (count:92 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:40836000-40843600	Weak transcription	Spleen	Spleen
2	chr5:40836000-40852600	Weak transcription	Small Intestine	intestine
3	chr5:40840800-40842800	Active TSS	Adipose Nuclei	Adipose
4	chr5:40841000-40842000	Active TSS	Primary hematopoietic stem cells	blood
5	chr5:40841000-40842000	Active TSS	Pancreatic Islets	Pancreatic Islet
6	chr5:40841000-40842200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
7	chr5:40841000-40842200	Active TSS	Primary T cells fromperipheralblood	blood
8	chr5:40841000-40842400	Active TSS	Rectal Mucosa Donor 29	rectum
9	chr5:40841000-40842800	Active TSS	Aorta	Aorta
10	chr5:40841000-40842800	Active TSS	Colon Smooth Muscle	Colon
11	chr5:40841000-40842800	Active TSS	Duodenum Smooth Muscle	Duodenum
12	chr5:40841000-40842800	Active TSS	Right Ventricle	heart
13	chr5:40841000-40842800	Active TSS	GM12878-XiMat	blood
14	chr5:40841200-40842000	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
15	chr5:40841200-40842000	Active TSS	Primary T killer memory cells from peripheral blood	blood
16	chr5:40841200-40842000	Active TSS	Skeletal Muscle Male	skeletal muscle
17	chr5:40841200-40842200	Bivalent/Poised TSS	Primary T regulatory cells fromperipheralblood	blood
18	chr5:40841200-40842200	Active TSS	Brain Cingulate Gyrus	brain
19	chr5:40841200-40842200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
20	chr5:40841200-40842200	Active TSS	Colonic Mucosa	Colon
21	chr5:40841200-40842200	Active TSS	Fetal Intestine Large	intestine
22	chr5:40841200-40842200	Active TSS	Fetal Kidney	kidney
23	chr5:40841200-40842200	Active TSS	Fetal Muscle Leg	muscle
24	chr5:40841200-40842200	Active TSS	Placenta	Placenta
25	chr5:40841200-40842200	Active TSS	Fetal Stomach	stomach
26	chr5:40841200-40842200	Active TSS	Rectal Mucosa Donor 31	rectum
27	chr5:40841200-40842200	Active TSS	Rectal Smooth Muscle	rectum
28	chr5:40841200-40842200	Active TSS	A549	lung
29	chr5:40841200-40842200	Active TSS	HepG2	liver
30	chr5:40841200-40842400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr5:40841200-40842400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr5:40841200-40842400	Active TSS	Brain Anterior Caudate	brain
33	chr5:40841200-40842400	Active TSS	Brain Hippocampus Middle	brain
34	chr5:40841200-40842400	Active TSS	Brain Substantia Nigra	brain
35	chr5:40841200-40842400	Active TSS	Ovary	ovary
36	chr5:40841200-40842600	Active TSS	Skeletal Muscle Female	skeletal muscle
37	chr5:40841200-40842800	Active TSS	Stomach Smooth Muscle	stomach
38	chr5:40841200-40842800	Active TSS	NHDF-Ad	bronchial
39	chr5:40841200-40843000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr5:40841200-40843200	Active TSS	Psoas Muscle	Psoas
41	chr5:40841200-40843600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr5:40841200-40844000	Active TSS	Right Atrium	heart
43	chr5:40841400-40842000	Active TSS	Primary monocytes fromperipheralblood	blood
44	chr5:40841400-40842000	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
45	chr5:40841400-40842000	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr5:40841400-40842000	Active TSS	Muscle Satellite Cultured Cells	--
47	chr5:40841400-40842000	Active TSS	Fetal Thymus	thymus
48	chr5:40841400-40842000	Active TSS	Hela-S3	cervix
49	chr5:40841400-40842000	Active TSS	Osteobl	bone
50	chr5:40841400-40842200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links