Variant report

Variant	rs3827551
Chromosome Location	chr2:86565467-86565468
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	KAP1	chr2:86565184-86565539	HEK293	kidney:	n/a	n/a

Variant related genes	Relation type
REEP1	TF binding region

Extended variants
information (count: 33 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10451666	1.00[CEU][hapmap]
rs12471787	0.82[LWK][hapmap]
rs17027263	1.00[CEU][hapmap];1.00[MEX][hapmap]
rs1863062	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs3731815	0.85[GIH][hapmap]
rs3731816	0.85[GIH][hapmap]
rs3731817	0.86[JPT][hapmap]
rs3770064	0.85[GIH][hapmap]
rs3821015	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs56661459	0.87[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs56988639	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs57503894	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs57933210	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs58522053	0.86[ASN][1000 genomes]
rs59676747	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs59744815	0.86[ASN][1000 genomes]
rs60177707	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs60386015	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs60904419	1.00[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs61231657	0.87[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs61627769	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6547678	0.86[ASN][1000 genomes]
rs6716825	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap]
rs6728494	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs6750561	0.87[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs6760222	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap]
rs7567955	0.87[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs7593666	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap]
rs7606682	1.00[CEU][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs7607280	0.86[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	esv3412938	chr2:86370969-86867936	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	77 gene(s)	inside rSNPs	diseases
2	esv3357801	chr2:86563266-86566214	Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	esv3448068	chr2:86563641-86565889	Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Flanking Active TSS Bivalent Enhancer Enhancers Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3827551	POLR1A	cis	lymphoblastoid	seeQTL

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:86563000-86565600	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
2	chr2:86563400-86565600	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
3	chr2:86563400-86565600	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
4	chr2:86563600-86565600	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
5	chr2:86563600-86565600	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
6	chr2:86563600-86565600	Active TSS	Pancreatic Islets	Pancreatic Islet
7	chr2:86564000-86565600	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
8	chr2:86564000-86565600	Bivalent/Poised TSS	Primary T cells from cord blood	blood
9	chr2:86564200-86565600	Active TSS	Lung	lung
10	chr2:86564800-86565600	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
11	chr2:86565000-86565600	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
12	chr2:86565000-86565600	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr2:86565000-86565600	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
14	chr2:86565000-86565600	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr2:86565000-86565600	Bivalent Enhancer	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr2:86565000-86565600	Bivalent Enhancer	Primary B cells from peripheral blood	blood
17	chr2:86565000-86565600	Bivalent Enhancer	Primary T killer memory cells from peripheral blood	blood
18	chr2:86565000-86565600	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr2:86565000-86565600	Flanking Active TSS	Brain Angular Gyrus	brain
20	chr2:86565000-86565600	Flanking Active TSS	Brain Anterior Caudate	brain
21	chr2:86565000-86565600	Flanking Active TSS	Brain Hippocampus Middle	brain
22	chr2:86565000-86565600	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
23	chr2:86565000-86565600	Flanking Active TSS	Fetal Brain Female	brain
24	chr2:86565000-86565600	Bivalent Enhancer	Sigmoid Colon	Sigmoid Colon
25	chr2:86565000-86565600	Bivalent Enhancer	Stomach Mucosa	stomach
26	chr2:86565000-86565600	Flanking Bivalent TSS/Enh	A549	lung
27	chr2:86565200-86565600	Bivalent Enhancer	Primary T cells effector/memory enriched fromperipheralblood	blood
28	chr2:86565200-86565600	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr2:86565200-86565600	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
30	chr2:86565200-86565600	Bivalent Enhancer	Colonic Mucosa	Colon
31	chr2:86565200-86565600	Flanking Active TSS	Fetal Brain Male	brain
32	chr2:86565200-86565600	Bivalent Enhancer	Fetal Intestine Small	intestine
33	chr2:86565200-86565600	Bivalent Enhancer	Placenta	Placenta
34	chr2:86565200-86565600	Bivalent Enhancer	Fetal Stomach	stomach
35	chr2:86565200-86565600	Enhancers	Psoas Muscle	Psoas
36	chr2:86565200-86565600	Bivalent Enhancer	Rectal Mucosa Donor 31	rectum
37	chr2:86565200-86565600	Bivalent Enhancer	NHEK	skin
38	chr2:86565200-86566200	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
39	chr2:86565400-86565600	Bivalent Enhancer	ES-WA7 Cell Line	embryonic stem cell
40	chr2:86565400-86565600	Bivalent Enhancer	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr2:86565400-86565600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
42	chr2:86565400-86565600	Flanking Bivalent TSS/Enh	Primary T helper naive cells fromperipheralblood	blood
43	chr2:86565400-86565600	Flanking Bivalent TSS/Enh	Primary T helper cells fromperipheralblood	blood
44	chr2:86565400-86565600	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr2:86565400-86565600	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr2:86565400-86565600	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr2:86565400-86565600	Active TSS	Brain Cingulate Gyrus	brain
48	chr2:86565400-86565600	Enhancers	Colon Smooth Muscle	Colon
49	chr2:86565400-86565600	Bivalent Enhancer	Duodenum Mucosa	Duodenum
50	chr2:86565400-86565600	Bivalent Enhancer	Fetal Intestine Large	intestine

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links