Variant report

Variant	rs34911788
Chromosome Location	chr2:171787250-171787251
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:171786011..171788954-chr2:172272838..172276305,3	K562	blood:
2	chr2:171784160..171787954-chr2:172288133..172292253,10	K562	blood:
3	chr2:171626961..171629009-chr2:171784250..171787377,4	K562	blood:
4	chr2:171787073..171789315-chr2:171814638..171817447,2	K562	blood:
5	chr2:171770754..171773506-chr2:171785657..171787829,2	K562	blood:
6	chr2:171786521..171789315-chr2:171814811..171817447,2	K562	blood:
7	chr2:171786681..171789668-chr2:172749612..172751986,2	K562	blood:
8	chr2:171784119..171787322-chr2:172288781..172292051,4	MCF-7	breast:
9	chr2:171783791..171787349-chr2:172286549..172291928,9	K562	blood:
10	chr2:171786011..171788954-chr2:172274093..172276305,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000239467	Chromatin interaction
ENSG00000123600	Chromatin interaction
ENSG00000234350	Chromatin interaction
ENSG00000115827	Chromatin interaction
ENSG00000266020	Chromatin interaction
ENSG00000115840	Chromatin interaction

Extended variants
information (count: 64 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs10515934	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10803853	1.00[ASN][1000 genomes]
rs10803854	0.94[ASN][1000 genomes]
rs10930448	0.94[ASN][1000 genomes]
rs10930449	0.94[ASN][1000 genomes]
rs12151587	0.81[ASN][1000 genomes]
rs12471930	0.94[ASN][1000 genomes]
rs12612871	0.94[ASN][1000 genomes]
rs12988738	0.83[ASN][1000 genomes]
rs12996518	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13000898	0.86[ASN][1000 genomes]
rs13011011	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13015226	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13026662	0.88[ASN][1000 genomes]
rs13028857	0.85[EUR][1000 genomes]
rs13035460	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1529391	0.94[ASN][1000 genomes]
rs16859066	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16859081	0.85[ASN][1000 genomes]
rs17281735	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2114738	0.88[ASN][1000 genomes]
rs2195116	0.91[ASN][1000 genomes]
rs2557799	0.88[ASN][1000 genomes]
rs34004615	0.85[ASN][1000 genomes]
rs34005022	0.83[EUR][1000 genomes]
rs34017170	0.85[ASN][1000 genomes]
rs34330182	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34342928	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34532258	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35123411	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35230775	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35864840	0.85[ASN][1000 genomes]
rs35890547	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35987434	0.88[ASN][1000 genomes]
rs3755125	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3770435	0.80[ASN][1000 genomes]
rs3770440	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3770441	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3770442	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3821090	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4668349	0.84[ASN][1000 genomes]
rs4668350	0.84[ASN][1000 genomes]
rs4668355	0.94[ASN][1000 genomes]
rs6433267	1.00[ASN][1000 genomes]
rs6709077	0.85[ASN][1000 genomes]
rs6714164	0.88[ASN][1000 genomes]
rs6714300	0.94[ASN][1000 genomes]
rs6715386	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6724493	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6729847	1.00[ASN][1000 genomes]
rs6734903	0.85[ASN][1000 genomes]
rs6742797	0.94[ASN][1000 genomes]
rs6743201	0.85[ASN][1000 genomes]
rs71415229	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71415231	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs71415232	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs71415233	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs731692	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs731693	0.94[ASN][1000 genomes]
rs73976229	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7570701	0.94[ASN][1000 genomes]
rs960222	0.81[ASN][1000 genomes]
rs965518	0.88[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv431801	chr2:171721493-171966493	ZNF genes & repeats Strong transcription Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs34911788	TLK1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:171784400-171787600	Active TSS	ES-I3 Cell Line	embryonic stem cell
2	chr2:171784800-171787400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
3	chr2:171784800-171787600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr2:171785000-171787400	Active TSS	Pancreatic Islets	Pancreatic Islet
5	chr2:171785000-171787400	Active TSS	Left Ventricle	heart
6	chr2:171785200-171787400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr2:171785200-171787400	Active TSS	HUES64 Cell Line	embryonic stem cell
8	chr2:171785200-171787400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr2:171785200-171787400	Active TSS	Breast Myoepithelial Primary Cells	Breast
10	chr2:171785200-171787400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr2:171785200-171787400	Active TSS	Colonic Mucosa	Colon
12	chr2:171785200-171787400	Active TSS	Esophagus	oesophagus
13	chr2:171785200-171787400	Active TSS	Pancreas	Pancrea
14	chr2:171785200-171787600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr2:171785200-171787600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr2:171785200-171787600	Active TSS	GM12878-XiMat	blood
17	chr2:171785200-171787600	Active TSS	HMEC	breast
18	chr2:171785200-171787600	Active TSS	NH-A	brain
19	chr2:171785200-171787600	Active TSS	NHDF-Ad	bronchial
20	chr2:171785200-171787800	Active TSS	HSMM	muscle
21	chr2:171785200-171788000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr2:171785200-171788000	Active TSS	NHLF	lung
23	chr2:171785400-171787600	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr2:171785400-171787600	Active TSS	Fetal Intestine Small	intestine
25	chr2:171785400-171787800	Active TSS	HUES6 Cell Line	embryonic stem cell
26	chr2:171785400-171787800	Active TSS	iPS-20b Cell Line	embryonic stem cell
27	chr2:171785400-171787800	Active TSS	HSMMtube	muscle
28	chr2:171785600-171787400	Active TSS	Lung	lung
29	chr2:171785800-171787400	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
30	chr2:171786000-171787600	Active TSS	Right Atrium	heart
31	chr2:171786200-171787400	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
32	chr2:171786400-171787400	Flanking Active TSS	Primary B cells from cord blood	blood
33	chr2:171786400-171787400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
34	chr2:171786400-171787600	Flanking Active TSS	Primary hematopoietic stem cells	blood
35	chr2:171786400-171787600	Flanking Active TSS	Stomach Smooth Muscle	stomach
36	chr2:171786400-171787800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr2:171786400-171787800	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
38	chr2:171786400-171788000	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr2:171786400-171788000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr2:171786600-171787400	Flanking Active TSS	Brain Germinal Matrix	brain
41	chr2:171786600-171787400	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
42	chr2:171786600-171787400	Flanking Active TSS	Brain Substantia Nigra	brain
43	chr2:171786600-171787400	Flanking Active TSS	Rectal Smooth Muscle	rectum
44	chr2:171786600-171787400	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
45	chr2:171786600-171787600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
46	chr2:171786600-171787600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr2:171786600-171787600	Flanking Active TSS	Adipose Nuclei	Adipose
48	chr2:171786600-171787600	Flanking Active TSS	Liver	Liver
49	chr2:171786600-171787600	Flanking Active TSS	Fetal Stomach	stomach
50	chr2:171786600-171787800	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links