Variant report

Variant	rs13013975
Chromosome Location	chr2:37813373-37813374
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:37807890..37810236-chr2:37813003..37815246,2	K562	blood:
2	chr2:37804698..37807657-chr2:37813185..37814836,2	K562	blood:
3	chr2:37810267..37812004-chr2:37812621..37814787,2	MCF-7	breast:

Extended variants
information (count: 16 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs10173816	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10184801	0.87[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs10208172	0.98[ASN][1000 genomes]
rs6708088	0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs740992	0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7560890	0.87[AFR][1000 genomes]
rs765372	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs983895	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv833814	chr2:37643132-37840247	Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv456374	chr2:37669487-37868214	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv470453	chr2:37669487-37868214	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv581473	chr2:37669487-37868214	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	esv2757793	chr2:37796654-38138939	Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
6	esv2759043	chr2:37796654-38138939	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
7	esv2762494	chr2:37802996-37813373	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
8	nsv833825	chr2:37808169-37985917	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs13013975	PRKD3	cis	cerebellum	SCAN
rs13013975	CDC42EP3	cis	parietal	SCAN
rs13013975	CDKL4	cis	parietal	SCAN

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:37808800-37818000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr2:37809400-37814600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
3	chr2:37809400-37814600	Enhancers	Fetal Thymus	thymus
4	chr2:37809400-37817600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr2:37809600-37816600	Enhancers	Osteobl	bone
6	chr2:37809800-37818400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr2:37810000-37817400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr2:37810000-37817600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr2:37810200-37814400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr2:37810200-37814600	Enhancers	NHLF	lung
11	chr2:37810200-37815800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
12	chr2:37810200-37816200	Enhancers	Breast Myoepithelial Primary Cells	Breast
13	chr2:37810200-37817800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr2:37810400-37814600	Enhancers	Placenta Amnion	Placenta Amnion
15	chr2:37810400-37815800	Enhancers	Primary T cells fromperipheralblood	blood
16	chr2:37810400-37815800	Enhancers	Primary T helper naive cells from peripheral blood	blood
17	chr2:37810600-37814400	Enhancers	Duodenum Smooth Muscle	Duodenum
18	chr2:37811000-37813800	Weak transcription	Primary hematopoietic stem cells	blood
19	chr2:37811000-37814200	Enhancers	Fetal Lung	lung
20	chr2:37811000-37815200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr2:37811200-37814400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr2:37811200-37814600	Enhancers	Thymus	Thymus
23	chr2:37811200-37817800	Enhancers	ES-I3 Cell Line	embryonic stem cell
24	chr2:37811400-37813800	Enhancers	HUVEC	blood vessel
25	chr2:37811400-37818400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr2:37811600-37813400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
27	chr2:37811600-37813400	Enhancers	Muscle Satellite Cultured Cells	--
28	chr2:37811600-37813600	Enhancers	NH-A	brain
29	chr2:37811600-37814400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr2:37811600-37814600	Enhancers	Stomach Mucosa	stomach
31	chr2:37811600-37817800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr2:37812000-37814200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
33	chr2:37812000-37814600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
34	chr2:37812000-37817400	Enhancers	Sigmoid Colon	Sigmoid Colon
35	chr2:37812000-37817600	Enhancers	iPS-15b Cell Line	embryonic stem cell
36	chr2:37812200-37813600	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
37	chr2:37812200-37813800	Flanking Active TSS	GM12878-XiMat	blood
38	chr2:37812200-37814200	Flanking Active TSS	A549	lung
39	chr2:37812200-37814200	Enhancers	K562	blood
40	chr2:37812200-37814400	Enhancers	H9 Cell Line	embryonic stem cell
41	chr2:37812200-37814400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
42	chr2:37812200-37814600	Enhancers	Primary hematopoietic stem cells short term culture	blood
43	chr2:37812200-37814800	Enhancers	Primary T cells from cord blood	blood
44	chr2:37812200-37817800	Enhancers	iPS-18 Cell Line	embryonic stem cell
45	chr2:37812400-37813400	Enhancers	Spleen	Spleen
46	chr2:37812400-37813600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
47	chr2:37812400-37813600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
48	chr2:37812400-37813600	Enhancers	Colonic Mucosa	Colon
49	chr2:37812400-37813600	Enhancers	Duodenum Mucosa	Duodenum
50	chr2:37812400-37813600	Enhancers	Placenta	Placenta

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links