Variant report

Variant	rs527393
Chromosome Location	chr2:169709757-169709758
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	CUX1	chr2:169709676-169709837	K562	blood:	n/a	n/a
2	JUN	chr2:169707367-169709802	K562	blood:	n/a	chr2:169709702-169709714 chr2:169709661-169709669 chr2:169709239-169709248
3	POLR2A	chr2:169701379-169710346	K562	blood:	n/a	n/a
4	BHLHE40	chr2:169709621-169709807	K562	blood:	n/a	n/a
5	GATA3	chr2:169709702-169710209	MCF-7	breast:	n/a	chr2:169709927-169709936

No.	Distal block	Cell Line	Cell type
1	chr2:169629254..169632077-chr2:169708619..169710261,2	K562	blood:
2	chr2:169708518..169710215-chr2:169719291..169720993,2	K562	blood:
3	chr2:169708194..169710093-chr2:169710266..169712297,2	K562	blood:

Variant related genes	Relation type
NOSTRIN	TF binding region
ENSG00000163072	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs2632380	0.99[ASN][1000 genomes]
rs2685799	0.81[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	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[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]
rs531328	0.80[ASN][1000 genomes]
rs540652	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs543727	0.89[ASN][1000 genomes]
rs546146	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs554494	0.98[ASN][1000 genomes]
rs560952	0.96[ASN][1000 genomes]
rs566465	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs569997	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs576062	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6734923	0.96[ASN][1000 genomes]
rs7582529	0.90[ASN][1000 genomes]
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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs527393	SPC25	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:169683400-169717600	Weak transcription	Ovary	ovary
2	chr2:169688000-169710600	Weak transcription	Fetal Muscle Leg	muscle
3	chr2:169689000-169721800	Weak transcription	Rectal Smooth Muscle	rectum
4	chr2:169693400-169721400	Weak transcription	Spleen	Spleen
5	chr2:169693600-169711200	Weak transcription	Lung	lung
6	chr2:169693600-169721400	Weak transcription	Right Ventricle	heart
7	chr2:169698400-169713000	Weak transcription	Fetal Heart	heart
8	chr2:169698400-169721200	Weak transcription	Stomach Mucosa	stomach
9	chr2:169698600-169744600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr2:169702200-169721200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
11	chr2:169702200-169733000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr2:169702600-169721400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr2:169703200-169713600	Weak transcription	HUES6 Cell Line	embryonic stem cell
14	chr2:169703600-169714600	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr2:169703600-169721200	Weak transcription	GM12878-XiMat	blood
16	chr2:169704200-169723400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr2:169704600-169721400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr2:169704800-169709800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr2:169705000-169721000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr2:169705000-169723600	Weak transcription	Fetal Brain Female	brain
21	chr2:169705200-169711400	Weak transcription	Pancreatic Islets	Pancreatic Islet
22	chr2:169705200-169721400	Weak transcription	Fetal Kidney	kidney
23	chr2:169706000-169719000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
24	chr2:169706200-169717600	Weak transcription	Pancreas	Pancrea
25	chr2:169706400-169711200	Weak transcription	NH-A	brain
26	chr2:169706400-169713000	Weak transcription	Psoas Muscle	Psoas
27	chr2:169706600-169713200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
28	chr2:169706600-169721600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
29	chr2:169706600-169727800	Weak transcription	Primary monocytes fromperipheralblood	blood
30	chr2:169706800-169711600	Strong transcription	Fetal Thymus	thymus
31	chr2:169706800-169713400	Strong transcription	Fetal Intestine Large	intestine
32	chr2:169706800-169718400	Weak transcription	Liver	Liver
33	chr2:169707000-169711600	Strong transcription	Duodenum Mucosa	Duodenum
34	chr2:169707000-169721000	Weak transcription	Cortex derived primary cultured neurospheres	brain
35	chr2:169707200-169712000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr2:169707200-169714800	Strong transcription	Rectal Mucosa Donor 29	rectum
37	chr2:169707400-169710200	Strong transcription	Adipose Nuclei	Adipose
38	chr2:169707400-169713400	Strong transcription	Dnd41	blood
39	chr2:169707400-169722000	Strong transcription	Rectal Mucosa Donor 31	rectum
40	chr2:169708200-169711400	Strong transcription	Fetal Intestine Small	intestine
41	chr2:169708400-169710000	Strong transcription	Placenta	Placenta
42	chr2:169708600-169712800	Weak transcription	Fetal Stomach	stomach
43	chr2:169708600-169712800	Weak transcription	Skeletal Muscle Male	skeletal muscle
44	chr2:169708600-169723200	Weak transcription	NHLF	lung
45	chr2:169708800-169710000	Weak transcription	Thymus	Thymus
46	chr2:169708800-169717600	Weak transcription	Gastric	stomach
47	chr2:169708800-169718400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr2:169708800-169721000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr2:169708800-169721200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr2:169708800-169721200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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