Variant report

Variant	rs540652
Chromosome Location	chr2:169707428-169707429
allele	C/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	JUN	chr2:169707367-169709802	K562	blood:	n/a	chr2:169709702-169709714 chr2:169709661-169709669 chr2:169709239-169709248
2	POLR2A	chr2:169701379-169710346	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:169702428..169704516-chr2:169706998..169708601,2	K562	blood:
2	chr2:169700277..169703960-chr2:169704282..169708601,6	K562	blood:

Variant related genes	Relation type
NOSTRIN	TF binding region

Extended variants
information (count: 25 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs2632380	0.99[ASN][1000 genomes]
rs2685799	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs480731	0.88[ASN][1000 genomes]
rs488621	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs493816	0.89[ASN][1000 genomes]
rs497808	1.00[ASN][1000 genomes]
rs506362	0.86[ASN][1000 genomes]
rs518337	0.80[ASN][1000 genomes]
rs527393	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs531328	0.80[ASN][1000 genomes]
rs543727	0.89[ASN][1000 genomes]
rs546146	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs554494	0.98[ASN][1000 genomes]
rs560952	0.96[ASN][1000 genomes]
rs566465	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs569997	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs576062	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6734923	0.96[ASN][1000 genomes]
rs7582529	0.90[ASN][1000 genomes]
rs830020	0.83[CHD][hapmap]
rs830193	0.90[ASN][1000 genomes]
rs9751269	0.89[ASN][1000 genomes]
rs9753196	0.87[ASN][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	nsv583599	chr2:169664227-169903096	Bivalent Enhancer Weak transcription Genic enhancers Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
2	nsv875381	chr2:169686559-169749841	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs540652	NOSTRIN	cis	Stomach	GTEx
rs540652	SPC25	cis	lymphoblastoid	seeQTL
rs540652	SSB	cis	cerebellum	SCAN
rs540652	G6PC2	cis	lung	GTEx
rs540652	SPC25	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:169676600-169709600	Weak transcription	Fetal Muscle Trunk	muscle
2	chr2:169683400-169717600	Weak transcription	Ovary	ovary
3	chr2:169688000-169710600	Weak transcription	Fetal Muscle Leg	muscle
4	chr2:169689000-169721800	Weak transcription	Rectal Smooth Muscle	rectum
5	chr2:169692000-169708400	Weak transcription	Colonic Mucosa	Colon
6	chr2:169693200-169707600	Weak transcription	Left Ventricle	heart
7	chr2:169693200-169708400	Weak transcription	Placenta	Placenta
8	chr2:169693400-169721400	Weak transcription	Spleen	Spleen
9	chr2:169693600-169707600	Weak transcription	Gastric	stomach
10	chr2:169693600-169711200	Weak transcription	Lung	lung
11	chr2:169693600-169721400	Weak transcription	Right Ventricle	heart
12	chr2:169694200-169708200	Weak transcription	Fetal Stomach	stomach
13	chr2:169698400-169713000	Weak transcription	Fetal Heart	heart
14	chr2:169698400-169721200	Weak transcription	Stomach Mucosa	stomach
15	chr2:169698600-169744600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr2:169702000-169708200	Weak transcription	Fetal Intestine Small	intestine
17	chr2:169702200-169721200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
18	chr2:169702200-169733000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr2:169702600-169721400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr2:169703200-169713600	Weak transcription	HUES6 Cell Line	embryonic stem cell
21	chr2:169703600-169714600	Weak transcription	Sigmoid Colon	Sigmoid Colon
22	chr2:169703600-169721200	Weak transcription	GM12878-XiMat	blood
23	chr2:169704000-169707600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr2:169704200-169723400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
25	chr2:169704600-169721400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr2:169704800-169709800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr2:169705000-169721000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr2:169705000-169723600	Weak transcription	Fetal Brain Female	brain
29	chr2:169705200-169708200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr2:169705200-169711400	Weak transcription	Pancreatic Islets	Pancreatic Islet
31	chr2:169705200-169721400	Weak transcription	Fetal Kidney	kidney
32	chr2:169705800-169708200	Weak transcription	Skeletal Muscle Male	skeletal muscle
33	chr2:169705800-169708200	Weak transcription	Thymus	Thymus
34	chr2:169706000-169707600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr2:169706000-169709000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr2:169706000-169719000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
37	chr2:169706200-169717600	Weak transcription	Pancreas	Pancrea
38	chr2:169706400-169711200	Weak transcription	NH-A	brain
39	chr2:169706400-169713000	Weak transcription	Psoas Muscle	Psoas
40	chr2:169706600-169708200	Genic enhancers	K562	blood
41	chr2:169706600-169708200	Weak transcription	Monocytes-CD14+_RO01746	blood
42	chr2:169706600-169713200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
43	chr2:169706600-169721600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
44	chr2:169706600-169727800	Weak transcription	Primary monocytes fromperipheralblood	blood
45	chr2:169706800-169708000	Weak transcription	NHEK	skin
46	chr2:169706800-169711600	Strong transcription	Fetal Thymus	thymus
47	chr2:169706800-169713400	Strong transcription	Fetal Intestine Large	intestine
48	chr2:169706800-169718400	Weak transcription	Liver	Liver
49	chr2:169707000-169708200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr2:169707000-169709600	Weak transcription	HepG2	liver

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links