Variant report

Variant	rs13408924
Chromosome Location	chr2:178979984-178979985
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:178978527..178980373-chr2:178984007..178986280,2	MCF-7	breast:
2	chr2:178974133..178981122-chr2:179276785..179281060,9	K562	blood:
3	chr2:178979115..178980922-chr2:179059390..179062250,2	K562	blood:
4	chr2:178978517..178980297-chr2:179707105..179709962,2	K562	blood:
5	chr2:178977795..178981676-chr2:178993113..178997821,5	K562	blood:
6	chr2:178978462..178980467-chr2:179057158..179058664,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000155636	Chromatin interaction
ENSG00000223960	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10176475	0.89[ASW][hapmap];0.94[CHB][hapmap];0.96[CHD][hapmap];0.94[JPT][hapmap];0.94[LWK][hapmap];0.95[MKK][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs10198111	0.82[CHB][hapmap]
rs10432485	0.88[JPT][hapmap]
rs11886139	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11887974	0.94[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs11899905	0.94[CHB][hapmap];0.94[JPT][hapmap]
rs1347441	0.83[CHB][hapmap]
rs1369515	0.94[CHB][hapmap];0.94[JPT][hapmap];0.95[ASN][1000 genomes]
rs1369517	0.88[CHB][hapmap];0.85[CHD][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs1435571	0.88[JPT][hapmap]
rs2034255	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2163647	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2217838	0.94[CHB][hapmap];0.94[JPT][hapmap]
rs4300869	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56103916	0.93[ASN][1000 genomes]
rs6433709	0.82[CHB][hapmap]
rs6709343	0.94[CHB][hapmap];0.94[JPT][hapmap]
rs6710329	0.94[CHB][hapmap];0.93[CHD][hapmap];0.94[JPT][hapmap];0.92[ASN][1000 genomes]
rs6714047	0.94[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs6738461	0.92[CHB][hapmap];0.92[JPT][hapmap]
rs6740828	0.93[ASN][1000 genomes]
rs6754705	0.93[ASN][1000 genomes]
rs736842	0.94[CHB][hapmap];0.94[JPT][hapmap]
rs7583491	0.93[CHB][hapmap];0.92[JPT][hapmap];0.93[ASN][1000 genomes]
rs9288014	0.94[CHB][hapmap];0.94[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1009312	chr2:178924318-179215566	Weak transcription Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv536057	chr2:178924318-179215566	Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv583739	chr2:178942302-178993562	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv518790	chr2:178963445-179000291	Weak transcription Flanking Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv875452	chr2:178963445-179167766	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13408924	PLEKHA3	cis	cerebellum	SCAN

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:178978000-178981000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
2	chr2:178978000-178984000	Weak transcription	Placenta	Placenta
3	chr2:178978000-178986600	Weak transcription	Left Ventricle	heart
4	chr2:178978000-178989200	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr2:178978000-178996600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr2:178978000-178996600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr2:178978000-179001000	Weak transcription	Lung	lung
8	chr2:178978000-179002200	Weak transcription	Esophagus	oesophagus
9	chr2:178978000-179003200	Weak transcription	Spleen	Spleen
10	chr2:178978000-179003800	Weak transcription	Aorta	Aorta
11	chr2:178978000-179016400	Weak transcription	Gastric	stomach
12	chr2:178978200-178980000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
13	chr2:178978200-178981000	Weak transcription	Fetal Muscle Trunk	muscle
14	chr2:178978200-178985400	Weak transcription	Fetal Thymus	thymus
15	chr2:178978200-178986200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr2:178978200-178986600	Weak transcription	Primary neutrophils fromperipheralblood	blood
17	chr2:178978200-178986800	Weak transcription	Psoas Muscle	Psoas
18	chr2:178978200-178990200	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr2:178978200-178997400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr2:178978200-179002800	Weak transcription	Fetal Stomach	stomach
21	chr2:178978400-178980200	Enhancers	Breast Myoepithelial Primary Cells	Breast
22	chr2:178978400-178980800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
23	chr2:178978400-178982000	Weak transcription	NH-A	brain
24	chr2:178978400-178982200	Weak transcription	Rectal Mucosa Donor 31	rectum
25	chr2:178978400-178983800	Weak transcription	Primary B cells from cord blood	blood
26	chr2:178978400-178986200	Weak transcription	HUES64 Cell Line	embryonic stem cell
27	chr2:178978400-178986400	Weak transcription	HUES48 Cell Line	embryonic stem cell
28	chr2:178978400-178986400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
29	chr2:178978400-178986600	Weak transcription	HUES6 Cell Line	embryonic stem cell
30	chr2:178978400-178986600	Weak transcription	Ovary	ovary
31	chr2:178978400-178988200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr2:178978400-178988200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr2:178978400-178988800	Weak transcription	HUVEC	blood vessel
34	chr2:178978400-178990000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
35	chr2:178978400-178990200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
36	chr2:178978400-178991800	Weak transcription	Colonic Mucosa	Colon
37	chr2:178978400-178997400	Weak transcription	H1 Cell Line	embryonic stem cell
38	chr2:178978400-179001200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
39	chr2:178978400-179001400	Weak transcription	Brain Substantia Nigra	brain
40	chr2:178978400-179001600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr2:178978400-179001800	Weak transcription	Brain Angular Gyrus	brain
42	chr2:178978600-178981000	Weak transcription	A549	lung
43	chr2:178978600-178981400	Weak transcription	Rectal Mucosa Donor 29	rectum
44	chr2:178978600-178982200	Weak transcription	Liver	Liver
45	chr2:178978600-178982200	Weak transcription	Brain Inferior Temporal Lobe	brain
46	chr2:178978600-178983600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr2:178978600-178984400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr2:178978600-178985600	Weak transcription	Stomach Smooth Muscle	stomach
49	chr2:178978600-178986400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
50	chr2:178978600-178986400	Weak transcription	Fetal Kidney	kidney

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links