Variant report

Variant	rs2171855
Chromosome Location	chr3:56789743-56789744
allele	C/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 14 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10222681	0.95[EUR][1000 genomes]
rs11130548	0.80[EUR][1000 genomes]
rs2171858	0.82[EUR][1000 genomes]
rs2276720	1.00[EUR][1000 genomes]
rs3732509	0.87[MEX][hapmap]
rs4619759	0.91[EUR][1000 genomes]
rs4681841	0.81[YRI][hapmap];0.93[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs6792241	0.95[CEU][hapmap];0.80[GIH][hapmap];0.92[MEX][hapmap];0.82[TSI][hapmap]
rs6794153	0.86[EUR][1000 genomes]
rs7627647	0.84[EUR][1000 genomes]
rs9825091	0.82[AMR][1000 genomes]
rs9851432	0.95[CEU][hapmap]
rs9851853	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9874011	0.93[EUR][1000 genomes]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2171855	ARF4	cis	parietal	SCAN

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:56757600-56792200	Weak transcription	Hela-S3	cervix
2	chr3:56758600-56792200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr3:56759800-56790400	Strong transcription	Dnd41	blood
4	chr3:56763800-56790200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr3:56763800-56792800	Weak transcription	Cortex derived primary cultured neurospheres	brain
6	chr3:56764000-56793400	Weak transcription	Gastric	stomach
7	chr3:56764000-56815800	Weak transcription	Fetal Intestine Small	intestine
8	chr3:56767400-56792600	Weak transcription	HUES6 Cell Line	embryonic stem cell
9	chr3:56768400-56797600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr3:56775000-56792600	Weak transcription	HUES64 Cell Line	embryonic stem cell
11	chr3:56779000-56792600	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr3:56781600-56792200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr3:56781600-56795200	Weak transcription	Brain Germinal Matrix	brain
14	chr3:56782200-56795200	Weak transcription	Lung	lung
15	chr3:56783400-56802800	Weak transcription	Brain Cingulate Gyrus	brain
16	chr3:56783600-56792600	Weak transcription	A549	lung
17	chr3:56783600-56802800	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr3:56783800-56802800	Weak transcription	Brain Hippocampus Middle	brain
19	chr3:56784400-56789800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr3:56784400-56792600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr3:56784600-56796400	Weak transcription	Fetal Brain Female	brain
22	chr3:56784800-56789800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr3:56785600-56792600	Weak transcription	Fetal Lung	lung
24	chr3:56786000-56789800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
25	chr3:56786000-56792200	Weak transcription	Stomach Mucosa	stomach
26	chr3:56786200-56789800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr3:56786400-56790000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr3:56787400-56792600	Weak transcription	Brain Anterior Caudate	brain
29	chr3:56787600-56789800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr3:56787600-56789800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr3:56787600-56790600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr3:56787600-56792600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr3:56787800-56790000	Flanking Active TSS	Primary B cells from cord blood	blood
34	chr3:56787800-56790400	Flanking Active TSS	Primary hematopoietic stem cells	blood
35	chr3:56788000-56790000	Weak transcription	HMEC	breast
36	chr3:56788000-56795600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr3:56788200-56789800	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
38	chr3:56788200-56790000	Transcr. at gene 5' and 3'	Primary T helper naive cells from peripheral blood	blood
39	chr3:56788200-56790000	Active TSS	Rectal Mucosa Donor 29	rectum
40	chr3:56788200-56790400	Genic enhancers	Fetal Muscle Leg	muscle
41	chr3:56788400-56789800	Flanking Active TSS	Primary T cells from cord blood	blood
42	chr3:56788400-56789800	Transcr. at gene 5' and 3'	Primary T helper cells PMA-I stimulated	--
43	chr3:56788400-56790000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
44	chr3:56788400-56790400	Genic enhancers	Brain Dorsolateral Prefrontal Cortex	brain
45	chr3:56788600-56789800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
46	chr3:56788600-56790400	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
47	chr3:56788800-56790000	Flanking Active TSS	Primary T cells fromperipheralblood	blood
48	chr3:56788800-56790000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
49	chr3:56788800-56790000	Enhancers	Fetal Kidney	kidney
50	chr3:56788800-56790000	Genic enhancers	Fetal Thymus	thymus

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links