Variant report

Variant	rs12711762
Chromosome Location	chr2:113932800-113932801
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:113930203..113932925-chr2:113950004..113952772,2	K562	blood:
2	chr2:113931492..113932996-chr2:113955583..113957836,2	MCF-7	breast:
3	chr2:113914021..113918016-chr2:113931911..113937619,8	MCF-7	breast:
4	chr2:113913340..113916449-chr2:113931202..113934969,5	MCF-7	breast:
5	chr2:113913826..113916797-chr2:113930139..113933348,3	K562	blood:

Variant related genes	Relation type
ENSG00000125637	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10864910	0.90[CEU][hapmap];0.81[AMR][1000 genomes]
rs11691876	0.81[AMR][1000 genomes]
rs12711765	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs1975535	0.83[CHB][hapmap];0.89[JPT][hapmap];0.85[ASN][1000 genomes]
rs2241976	0.83[ASN][1000 genomes]
rs3748914	0.91[CHB][hapmap];0.94[JPT][hapmap];0.87[ASN][1000 genomes]
rs4848316	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4849163	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4849166	0.91[CHB][hapmap];0.94[JPT][hapmap];0.87[ASN][1000 genomes]
rs4849167	0.91[CHB][hapmap];0.94[JPT][hapmap];0.87[ASN][1000 genomes]
rs4849168	0.83[CHB][hapmap];0.81[ASN][1000 genomes]
rs6737029	0.86[ASN][1000 genomes]
rs6750127	0.86[ASN][1000 genomes]
rs6760120	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6761202	0.91[CHB][hapmap];0.89[JPT][hapmap];0.87[ASN][1000 genomes]
rs7595962	0.95[CEU][hapmap];0.91[CHB][hapmap];0.94[JPT][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv997348	chr2:113688093-113986508	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
2	nsv582711	chr2:113895516-113984503	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
3	nsv582712	chr2:113932431-113985170	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12711762	PSD4	cis	Whole Blood	GTEx
rs12711762	PSD4	cis	Skin Sun Exposed Lower leg	GTEx
rs12711762	PSD4	cis	Esophagus Mucosa	GTEx

Chromatin state (count:75 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:113916000-113939000	Weak transcription	Right Atrium	heart
2	chr2:113923000-113951800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr2:113923000-113956000	Weak transcription	HMEC	breast
4	chr2:113923800-113937800	Weak transcription	H1 Cell Line	embryonic stem cell
5	chr2:113927600-113936200	Weak transcription	NHEK	skin
6	chr2:113928000-113935800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr2:113929600-113932800	Enhancers	Stomach Mucosa	stomach
8	chr2:113930200-113935200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr2:113930400-113934200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
10	chr2:113930600-113934200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr2:113930600-113934600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
12	chr2:113930800-113934000	Flanking Active TSS	Primary B cells from cord blood	blood
13	chr2:113930800-113937800	Weak transcription	Pancreas	Pancrea
14	chr2:113931000-113933600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
15	chr2:113931000-113933800	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
16	chr2:113931000-113934000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr2:113931000-113934200	Flanking Active TSS	Primary hematopoietic stem cells	blood
18	chr2:113931000-113934200	Active TSS	Rectal Smooth Muscle	rectum
19	chr2:113931000-113934400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
20	chr2:113931000-113935000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr2:113931200-113934000	Active TSS	Rectal Mucosa Donor 31	rectum
22	chr2:113931200-113934200	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
23	chr2:113931400-113933000	Active TSS	Duodenum Mucosa	Duodenum
24	chr2:113931400-113933200	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
25	chr2:113931400-113933200	Active TSS	GM12878-XiMat	blood
26	chr2:113931400-113933400	Active TSS	Primary T helper naive cells from peripheral blood	blood
27	chr2:113931400-113933400	Active TSS	Primary T killer memory cells from peripheral blood	blood
28	chr2:113931400-113933600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr2:113931400-113933800	Active TSS	Thymus	Thymus
30	chr2:113931400-113936200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr2:113931400-113937800	Weak transcription	Fetal Intestine Large	intestine
32	chr2:113931600-113932800	Active TSS	Spleen	Spleen
33	chr2:113931600-113933000	Active TSS	Primary T helper cells PMA-I stimulated	--
34	chr2:113931600-113933000	Active TSS	Brain Hippocampus Middle	brain
35	chr2:113931600-113933000	Active TSS	Stomach Smooth Muscle	stomach
36	chr2:113931600-113933200	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
37	chr2:113931600-113933200	Active TSS	Liver	Liver
38	chr2:113931600-113933400	Active TSS	Sigmoid Colon	Sigmoid Colon
39	chr2:113931600-113933400	Active TSS	Small Intestine	intestine
40	chr2:113931600-113933600	Active TSS	Duodenum Smooth Muscle	Duodenum
41	chr2:113931600-113933800	Active TSS	Esophagus	oesophagus
42	chr2:113931600-113934200	Active TSS	Colonic Mucosa	Colon
43	chr2:113931600-113934400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
44	chr2:113931800-113932800	Active TSS	Primary T helper naive cells fromperipheralblood	blood
45	chr2:113931800-113933800	Weak transcription	Fetal Lung	lung
46	chr2:113932000-113933600	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
47	chr2:113932000-113933600	Flanking Active TSS	Primary T cells fromperipheralblood	blood
48	chr2:113932000-113933600	Weak transcription	Lung	lung
49	chr2:113932000-113934200	Flanking Active TSS	Primary B cells from peripheral blood	blood
50	chr2:113932000-113935200	Transcr. at gene 5' and 3'	Dnd41	blood

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