Variant report

Variant	rs34686786
Chromosome Location	chr3:142217320-142217321
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 28 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs28897764	1.00[AMR][1000 genomes]
rs28897765	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28910270	1.00[AMR][1000 genomes]
rs28910271	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28910272	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs34104088	0.81[AFR][1000 genomes]
rs34213965	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs34383865	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs34678750	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs35264204	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs35363608	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs35404216	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs35440390	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs35988759	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs35993426	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs36090479	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7618253	0.95[EUR][1000 genomes]
rs7624616	0.95[EUR][1000 genomes]
rs7646257	0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv877556	chr3:141898980-142331360	Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv523945	chr3:141933649-142219542	Enhancers Genic enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
3	nsv877558	chr3:142123841-142331360	Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
4	nsv877559	chr3:142132749-142331360	Active TSS Enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
5	nsv877560	chr3:142132749-142362179	Strong transcription ZNF genes & repeats Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
6	nsv877561	chr3:142152925-142331360	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
7	nsv528954	chr3:142164017-142219542	ZNF genes & repeats Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
8	nsv932989	chr3:142204208-142423305	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
9	nsv933680	chr3:142211643-142287189	Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs34686786	PLS1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:142167400-142234600	Weak transcription	Psoas Muscle	Psoas
2	chr3:142200000-142223200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr3:142200400-142243800	Weak transcription	Fetal Heart	heart
4	chr3:142200600-142271800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr3:142200800-142219800	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr3:142201000-142218200	Strong transcription	Adipose Nuclei	Adipose
7	chr3:142201000-142218600	Strong transcription	Fetal Thymus	thymus
8	chr3:142201000-142239600	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr3:142201000-142240600	Weak transcription	Fetal Brain Male	brain
10	chr3:142201200-142218000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr3:142201200-142226800	Strong transcription	Primary T helper cells fromperipheralblood	blood
12	chr3:142201600-142218600	Strong transcription	Rectal Mucosa Donor 29	rectum
13	chr3:142201600-142219000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
14	chr3:142201600-142273200	Weak transcription	Esophagus	oesophagus
15	chr3:142201800-142218000	Strong transcription	Duodenum Mucosa	Duodenum
16	chr3:142201800-142240600	Weak transcription	Primary neutrophils fromperipheralblood	blood
17	chr3:142201800-142243600	Strong transcription	Monocytes-CD14+_RO01746	blood
18	chr3:142201800-142273800	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr3:142202000-142221200	Strong transcription	Primary B cells from peripheral blood	blood
20	chr3:142202000-142223800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
21	chr3:142202000-142231000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr3:142202000-142235200	Strong transcription	Primary monocytes fromperipheralblood	blood
23	chr3:142202000-142239600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr3:142202200-142218000	Strong transcription	Fetal Intestine Large	intestine
25	chr3:142202200-142218600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr3:142202200-142240200	Weak transcription	Colon Smooth Muscle	Colon
27	chr3:142202400-142219400	Strong transcription	Dnd41	blood
28	chr3:142202600-142218200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr3:142202800-142218200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
30	chr3:142202800-142219000	Strong transcription	Primary T cells fromperipheralblood	blood
31	chr3:142203000-142255200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
32	chr3:142203200-142218000	Strong transcription	HUES64 Cell Line	embryonic stem cell
33	chr3:142203600-142218200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr3:142203800-142223000	Weak transcription	Lung	lung
35	chr3:142203800-142225400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr3:142203800-142255200	Weak transcription	Gastric	stomach
37	chr3:142204200-142228000	Weak transcription	Pancreas	Pancrea
38	chr3:142204200-142253000	Weak transcription	Brain Substantia Nigra	brain
39	chr3:142204200-142273200	Weak transcription	Spleen	Spleen
40	chr3:142204200-142281400	Weak transcription	Colonic Mucosa	Colon
41	chr3:142206200-142217800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
42	chr3:142206400-142217800	Weak transcription	Fetal Intestine Small	intestine
43	chr3:142206600-142218000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr3:142206600-142219200	Strong transcription	Primary T helper cells PMA-I stimulated	--
45	chr3:142206800-142218000	Strong transcription	Duodenum Smooth Muscle	Duodenum
46	chr3:142207200-142217600	Strong transcription	Primary hematopoietic stem cells	blood
47	chr3:142207200-142217800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
48	chr3:142207400-142238600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr3:142208200-142226600	Strong transcription	Primary B cells from cord blood	blood
50	chr3:142208400-142231000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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