Variant report

Variant	rs1136995
Chromosome Location	chr3:121661597-121661598
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 6 )
Associated
traits (count: 14 )

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs12386356	1.00[ASN][1000 genomes]
rs9818226	0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9859192	0.89[EUR][1000 genomes]
rs9868875	0.88[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv516233	chr3:121419301-121670405	Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Enhancers Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
2	esv33139	chr3:121500400-122091831	Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:14)

SNP	Gene	Cis/trans	Tissue	Source
rs1136995	GOLGB1	cis	multi-tissue	Pritchard
rs1136995	GOLGB1	cis	Brain Pons	GTEx
rs1136995	SLC15A2	cis	hippocampus	BrainEAC
rs1136995	EAF2	Cis_1M	lymphoblastoid	RTeQTL
rs1136995	GOLGB1	cis	Frontal Cortex	GTEx
rs1136995	SLC15A2	cis	parietal	SCAN
rs1136995	IQCB1	cis	parietal	SCAN
rs1136995	SLC15A2	cis	brain	BrainEAC
rs1136995	IQCB1	Cis_1M	lymphoblastoid	RTeQTL
rs1136995	SLC15A2	cis	frontal cortex	BrainEAC
rs1136995	GOLGB1	cis	Temporal Cortex	GTEx
rs1136995	GOLGB1	cis	Cerebellum	GTEx
rs1136995	IQCB1	cis	cerebellum	SCAN
rs1136995	SLC15A2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:121615800-121671600	Weak transcription	Pancreas	Pancrea
2	chr3:121627400-121664600	Weak transcription	Aorta	Aorta
3	chr3:121631800-121664800	Weak transcription	Brain Angular Gyrus	brain
4	chr3:121634800-121667000	Weak transcription	Brain Cingulate Gyrus	brain
5	chr3:121635000-121670600	Weak transcription	Brain Hippocampus Middle	brain
6	chr3:121635200-121666800	Weak transcription	Brain Substantia Nigra	brain
7	chr3:121638400-121664800	Weak transcription	Spleen	Spleen
8	chr3:121642400-121661600	Weak transcription	Fetal Thymus	thymus
9	chr3:121646600-121661800	Weak transcription	Ovary	ovary
10	chr3:121646800-121666200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr3:121650600-121665800	Weak transcription	Duodenum Smooth Muscle	Duodenum
12	chr3:121650600-121675600	Weak transcription	Brain Anterior Caudate	brain
13	chr3:121651200-121664000	Weak transcription	Skeletal Muscle Female	skeletal muscle
14	chr3:121656400-121667200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr3:121656800-121675200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr3:121657000-121664600	Strong transcription	Primary neutrophils fromperipheralblood	blood
17	chr3:121657200-121662600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
18	chr3:121657600-121662600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr3:121657600-121663200	Strong transcription	Primary B cells from peripheral blood	blood
20	chr3:121657600-121663600	Strong transcription	Monocytes-CD14+_RO01746	blood
21	chr3:121657600-121666000	Strong transcription	Primary B cells from cord blood	blood
22	chr3:121657800-121665200	Strong transcription	Primary monocytes fromperipheralblood	blood
23	chr3:121658000-121667000	Strong transcription	Primary hematopoietic stem cells	blood
24	chr3:121659400-121662800	Enhancers	Placenta Amnion	Placenta Amnion
25	chr3:121659600-121661600	Weak transcription	GM12878-XiMat	blood
26	chr3:121659800-121661800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr3:121660000-121661600	Weak transcription	Duodenum Mucosa	Duodenum
28	chr3:121660000-121661800	Weak transcription	Placenta	Placenta
29	chr3:121660200-121661800	Weak transcription	Fetal Muscle Trunk	muscle
30	chr3:121660200-121664000	Weak transcription	Primary T cells from cord blood	blood
31	chr3:121660200-121666200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
32	chr3:121660200-121666400	Weak transcription	Lung	lung
33	chr3:121660200-121666800	Weak transcription	Fetal Muscle Leg	muscle
34	chr3:121660200-121670000	Weak transcription	Sigmoid Colon	Sigmoid Colon
35	chr3:121660200-121671600	Weak transcription	Left Ventricle	heart
36	chr3:121660200-121675200	Weak transcription	Brain Inferior Temporal Lobe	brain
37	chr3:121660200-121676600	Weak transcription	Cortex derived primary cultured neurospheres	brain
38	chr3:121660600-121661800	Enhancers	Fetal Intestine Large	intestine
39	chr3:121660600-121661800	Enhancers	Fetal Intestine Small	intestine
40	chr3:121660600-121670400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr3:121660800-121662600	Enhancers	NHEK	skin
42	chr3:121661000-121661600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr3:121661000-121661800	Enhancers	HUES48 Cell Line	embryonic stem cell
44	chr3:121661000-121661800	Enhancers	iPS-18 Cell Line	embryonic stem cell
45	chr3:121661000-121662800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr3:121661200-121661800	Enhancers	HUES64 Cell Line	embryonic stem cell
47	chr3:121661200-121661800	Enhancers	HMEC	breast
48	chr3:121661200-121662400	Weak transcription	Fetal Kidney	kidney
49	chr3:121661200-121663000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin

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