Variant report

Variant	rs2366366
Chromosome Location	chr2:178993213-178993214
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:178991876..178994492-chr2:179011398..179013023,2	K562	blood:
2	chr2:178977795..178981676-chr2:178993113..178997821,5	K562	blood:
3	chr2:178993079..178995697-chr2:179002423..179004658,2	K562	blood:
4	chr2:178987630..178989492-chr2:178991140..178993708,2	K562	blood:
5	chr2:178991568..178995332-chr2:178996165..178998325,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000155636	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs1025446	0.90[JPT][hapmap]
rs10930827	0.91[MEX][hapmap]
rs12613853	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12617847	0.95[CHB][hapmap];0.85[JPT][hapmap];0.89[ASN][1000 genomes]
rs12619532	0.91[CHB][hapmap];0.95[CHD][hapmap];0.85[JPT][hapmap];0.88[ASN][1000 genomes]
rs13005772	0.92[ASN][1000 genomes]
rs13006877	0.90[JPT][hapmap];0.80[MEX][hapmap]
rs1435572	0.91[CHB][hapmap];0.93[CHD][hapmap];0.85[JPT][hapmap];0.86[ASN][1000 genomes]
rs16866111	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs16866116	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs16866118	0.91[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs2276622	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs334062	0.95[JPT][hapmap];0.80[MEX][hapmap]
rs334068	0.95[JPT][hapmap]
rs62176035	0.88[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs6705312	0.91[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs6753254	0.88[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs7564892	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7582796	0.80[ASN][1000 genomes]

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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2366366	FKBP7	cis	parietal	SCAN
rs2366366	HOXD12	cis	parietal	SCAN
rs2366366	GPR155	cis	cerebellum	SCAN

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:178978000-178996600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr2:178978000-178996600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr2:178978000-179001000	Weak transcription	Lung	lung
4	chr2:178978000-179002200	Weak transcription	Esophagus	oesophagus
5	chr2:178978000-179003200	Weak transcription	Spleen	Spleen
6	chr2:178978000-179003800	Weak transcription	Aorta	Aorta
7	chr2:178978000-179016400	Weak transcription	Gastric	stomach
8	chr2:178978200-178997400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr2:178978200-179002800	Weak transcription	Fetal Stomach	stomach
10	chr2:178978400-178997400	Weak transcription	H1 Cell Line	embryonic stem cell
11	chr2:178978400-179001200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr2:178978400-179001400	Weak transcription	Brain Substantia Nigra	brain
13	chr2:178978400-179001600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr2:178978400-179001800	Weak transcription	Brain Angular Gyrus	brain
15	chr2:178978600-178996000	Weak transcription	Stomach Mucosa	stomach
16	chr2:178978600-178998400	Weak transcription	Brain Cingulate Gyrus	brain
17	chr2:178978600-179001800	Weak transcription	Hela-S3	cervix
18	chr2:178978600-179003000	Weak transcription	Right Ventricle	heart
19	chr2:178978600-179003600	Weak transcription	Fetal Heart	heart
20	chr2:178978800-178993800	Weak transcription	HSMMtube	muscle
21	chr2:178978800-178997200	Weak transcription	NHEK	skin
22	chr2:178978800-179001000	Weak transcription	Pancreas	Pancrea
23	chr2:178978800-179004000	Weak transcription	Brain Germinal Matrix	brain
24	chr2:178979000-178995000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr2:178979000-179005400	Weak transcription	Pancreatic Islets	Pancreatic Islet
26	chr2:178979600-178998800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr2:178980600-178995200	Strong transcription	Primary T helper cells fromperipheralblood	blood
28	chr2:178981000-178994600	Strong transcription	Primary monocytes fromperipheralblood	blood
29	chr2:178981000-178995000	Strong transcription	Monocytes-CD14+_RO01746	blood
30	chr2:178981000-178995600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
31	chr2:178981000-178995600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr2:178982000-178995200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr2:178982000-178995200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr2:178982200-178994600	Strong transcription	Liver	Liver
35	chr2:178982200-178995400	Strong transcription	Primary B cells from peripheral blood	blood
36	chr2:178982600-178995200	Strong transcription	Dnd41	blood
37	chr2:178983400-178995000	Strong transcription	Primary T cells fromperipheralblood	blood
38	chr2:178983800-178995800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
39	chr2:178983800-178996600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
40	chr2:178984800-178994600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
41	chr2:178985400-178994200	Strong transcription	Fetal Thymus	thymus
42	chr2:178986200-178994400	Strong transcription	Primary T cells from cord blood	blood
43	chr2:178987200-179005800	Weak transcription	Psoas Muscle	Psoas
44	chr2:178987400-179002800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr2:178987800-179017000	Weak transcription	Fetal Lung	lung
46	chr2:178988400-179001800	Weak transcription	NHDF-Ad	bronchial
47	chr2:178988400-179002000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
48	chr2:178988600-179002800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
49	chr2:178988800-178993600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr2:178988800-178996800	Weak transcription	Fetal Brain Male	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links