Variant report

Variant	rs574785
Chromosome Location	chr3:43119288-43119289
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 8 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs12233414	1.00[ASW][hapmap];0.84[LWK][hapmap];0.90[YRI][hapmap];0.82[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs503100	1.00[LWK][hapmap];1.00[MKK][hapmap];0.89[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs520446	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs535994	0.89[MKK][hapmap]
rs552472	0.89[MKK][hapmap]
rs679550	1.00[AFR][1000 genomes];1.00[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	nsv460522	chr3:42967597-43175207	Weak transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv590149	chr3:42967597-43175207	Flanking Active TSS ZNF genes & repeats Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs574785	PTK2	trans	lymphoblastoid	seeQTL
rs574785	TSPAN1	trans	lymphoblastoid	seeQTL
rs574785	OSBPL10	trans	lymphoblastoid	seeQTL
rs574785	IFNGR1	trans	lymphoblastoid	seeQTL
rs574785	IL6R	trans	lymphoblastoid	seeQTL

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:43093400-43120200	Weak transcription	Brain Cingulate Gyrus	brain
2	chr3:43096200-43121200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr3:43100200-43120200	Weak transcription	Brain Angular Gyrus	brain
4	chr3:43101600-43121000	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr3:43102000-43121000	Weak transcription	Duodenum Smooth Muscle	Duodenum
6	chr3:43103000-43120000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr3:43103200-43120600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
8	chr3:43104800-43120800	Weak transcription	Gastric	stomach
9	chr3:43105000-43119600	Weak transcription	Stomach Smooth Muscle	stomach
10	chr3:43106400-43120400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr3:43112200-43121200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr3:43112800-43120600	Weak transcription	Primary T helper cells PMA-I stimulated	--
13	chr3:43113000-43120800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr3:43115000-43120400	Weak transcription	Fetal Intestine Small	intestine
15	chr3:43115600-43119600	Weak transcription	Fetal Muscle Trunk	muscle
16	chr3:43116000-43120800	Weak transcription	Dnd41	blood
17	chr3:43116000-43121000	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr3:43116000-43121000	Weak transcription	Primary T cells fromperipheralblood	blood
19	chr3:43116200-43119400	Weak transcription	Primary T cells from cord blood	blood
20	chr3:43116600-43119600	Weak transcription	Lung	lung
21	chr3:43117000-43119600	Weak transcription	Skeletal Muscle Male	skeletal muscle
22	chr3:43117000-43119800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr3:43117000-43120200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr3:43117000-43121200	Weak transcription	Muscle Satellite Cultured Cells	--
25	chr3:43117200-43120200	Weak transcription	Fetal Thymus	thymus
26	chr3:43117200-43120800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr3:43117200-43121000	Weak transcription	Right Ventricle	heart
28	chr3:43117400-43119600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
29	chr3:43117400-43121000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr3:43117600-43120000	Weak transcription	Left Ventricle	heart
31	chr3:43117600-43120800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr3:43117600-43121000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr3:43117600-43121000	Weak transcription	Sigmoid Colon	Sigmoid Colon
34	chr3:43117800-43120200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr3:43117800-43120400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr3:43117800-43121000	Weak transcription	Esophagus	oesophagus
37	chr3:43118000-43120800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr3:43118000-43121200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr3:43118000-43121200	Weak transcription	Rectal Smooth Muscle	rectum
40	chr3:43118200-43120000	Weak transcription	Skeletal Muscle Female	skeletal muscle
41	chr3:43118200-43120800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
42	chr3:43118200-43121000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr3:43118200-43121000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr3:43118200-43121000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr3:43118200-43124800	Weak transcription	Pancreatic Islets	Pancreatic Islet
46	chr3:43118200-43128000	Weak transcription	Placenta Amnion	Placenta Amnion
47	chr3:43118400-43120200	Weak transcription	Adipose Nuclei	Adipose
48	chr3:43118400-43120600	Weak transcription	Liver	Liver
49	chr3:43118400-43120800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr3:43118400-43121000	Weak transcription	HUES64 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links