Variant report

Variant	rs2372887
Chromosome Location	chr2:37457012-37457013
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:7)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:7 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr2:37456880-37457030	SK-N-SH_RA	brain:	n/a	n/a
2	MXI1	chr2:37456226-37460228	SK-N-SH	brain:	n/a	n/a
3	CTCF	chr2:37456880-37457030	HCT-116	colon:	n/a	n/a
4	CTCF	chr2:37456842-37457095	GM12878	blood:	n/a	n/a
5	CTCF	chr2:37456880-37457030	GM12864	blood:	n/a	n/a
6	CTCF	chr2:37456900-37457050	GM12873	blood:	n/a	n/a
7	CTCF	chr2:37456880-37457030	GM06990	blood:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:37438602..37441837-chr2:37456700..37460160,3	K562	blood:
2	chr2:37422039..37425278-chr2:37456815..37459935,9	MCF-7	breast:
3	chr2:37454643..37457253-chr2:37471723..37474607,2	K562	blood:
4	chr2:37427347..37429134-chr2:37454276..37457065,3	MCF-7	breast:
5	chr2:37422594..37426591-chr2:37455893..37460210,5	MCF-7	breast:
6	chr2:37456368..37460350-chr2:37466636..37472512,8	MCF-7	breast:

No data

Variant related genes	Relation type
NDUFAF7	TF binding region
ENSG00000138068	Chromatin interaction
ENSG00000115816	Chromatin interaction
ENSG00000003509	Chromatin interaction
ENSG00000218739	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10206380	0.89[ASN][1000 genomes]
rs11124570	0.80[ASN][1000 genomes]
rs12476195	0.86[ASN][1000 genomes]
rs13429526	0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs17020344	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17020358	0.87[ASN][1000 genomes]
rs2041838	0.85[ASN][1000 genomes]
rs2041839	0.84[ASN][1000 genomes]
rs2075215	0.95[ASN][1000 genomes]
rs2075216	0.94[ASN][1000 genomes]
rs2300896	0.97[ASN][1000 genomes]
rs3213746	0.97[ASN][1000 genomes]
rs59559471	0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs59612622	0.87[ASN][1000 genomes]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2372887	PRKD3	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:37448400-37457800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr2:37453400-37457600	Transcr. at gene 5' and 3'	HUES48 Cell Line	embryonic stem cell
3	chr2:37455800-37457200	Weak transcription	Brain Anterior Caudate	brain
4	chr2:37455800-37457200	Weak transcription	Brain Hippocampus Middle	brain
5	chr2:37455800-37457600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr2:37455800-37457600	Weak transcription	Fetal Muscle Trunk	muscle
7	chr2:37455800-37457800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr2:37455800-37457800	Weak transcription	Esophagus	oesophagus
9	chr2:37455800-37457800	Weak transcription	Lung	lung
10	chr2:37456000-37457200	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
11	chr2:37456000-37457600	Enhancers	Primary T killer memory cells from peripheral blood	blood
12	chr2:37456200-37457400	Transcr. at gene 5' and 3'	HUES64 Cell Line	embryonic stem cell
13	chr2:37456200-37459600	Active TSS	iPS-20b Cell Line	embryonic stem cell
14	chr2:37456400-37457400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
15	chr2:37456400-37457400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
16	chr2:37456400-37457400	Enhancers	Cortex derived primary cultured neurospheres	brain
17	chr2:37456400-37457600	Enhancers	Primary neutrophils fromperipheralblood	blood
18	chr2:37456400-37457800	Flanking Active TSS	NHEK	skin
19	chr2:37456400-37458000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr2:37456600-37457200	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr2:37456600-37457200	Enhancers	Primary T helper naive cells from peripheral blood	blood
22	chr2:37456600-37457200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr2:37456600-37457200	Enhancers	Colonic Mucosa	Colon
24	chr2:37456600-37457200	Enhancers	Duodenum Mucosa	Duodenum
25	chr2:37456600-37457200	Enhancers	Pancreatic Islets	Pancreatic Islet
26	chr2:37456600-37457200	Flanking Active TSS	Psoas Muscle	Psoas
27	chr2:37456600-37457200	Enhancers	Rectal Smooth Muscle	rectum
28	chr2:37456600-37457200	Enhancers	Right Atrium	heart
29	chr2:37456600-37457200	Genic enhancers	Sigmoid Colon	Sigmoid Colon
30	chr2:37456600-37457200	Enhancers	NHDF-Ad	bronchial
31	chr2:37456600-37457400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr2:37456600-37457400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr2:37456600-37457400	Enhancers	Aorta	Aorta
34	chr2:37456600-37457400	Enhancers	Liver	Liver
35	chr2:37456600-37457400	Enhancers	Brain Angular Gyrus	brain
36	chr2:37456600-37457400	Enhancers	Fetal Lung	lung
37	chr2:37456600-37457400	Enhancers	Fetal Thymus	thymus
38	chr2:37456600-37457400	Enhancers	Stomach Mucosa	stomach
39	chr2:37456600-37457400	Flanking Active TSS	HepG2	liver
40	chr2:37456600-37457400	Flanking Active TSS	HMEC	breast
41	chr2:37456600-37457400	Enhancers	Osteobl	bone
42	chr2:37456600-37457600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr2:37456600-37457600	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
44	chr2:37456600-37457600	Enhancers	Primary monocytes fromperipheralblood	blood
45	chr2:37456600-37457600	Enhancers	Primary hematopoietic stem cells	blood
46	chr2:37456600-37457600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
47	chr2:37456600-37457600	Enhancers	Brain Inferior Temporal Lobe	brain
48	chr2:37456600-37457600	Enhancers	Left Ventricle	heart
49	chr2:37456600-37457600	Enhancers	Placenta Amnion	Placenta Amnion
50	chr2:37456600-37457600	Enhancers	Skeletal Muscle Male	skeletal muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links