Variant report

Variant	rs68018658
Chromosome Location	chr3:136391627-136391628
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:136388635..136392149-chr3:136467930..136472508,4	K562	blood:
2	chr3:136389835..136392302-chr3:136408179..136409824,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000118007	Chromatin interaction
ENSG00000261758	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10513016	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16844056	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17365351	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17466223	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55763637	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56218376	0.88[AFR][1000 genomes]
rs56308712	0.82[EUR][1000 genomes]
rs56888009	0.97[EUR][1000 genomes]
rs57466072	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57681357	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58636237	0.83[EUR][1000 genomes]
rs59361983	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs59616231	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59696368	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60014495	0.94[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs60270684	0.82[AFR][1000 genomes]
rs66470158	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66471262	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66637228	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66739346	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66902780	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs66973954	0.94[AFR][1000 genomes]
rs67231188	0.94[AFR][1000 genomes];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67236827	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67281610	0.86[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs67303976	0.94[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs67305360	0.94[AFR][1000 genomes]
rs67546863	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs67621498	0.88[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs67663578	0.94[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs6773495	0.94[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs67794070	0.94[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs67888773	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs67902591	0.83[EUR][1000 genomes]
rs67923745	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs72975363	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs73228025	0.90[EUR][1000 genomes]
rs73228037	0.93[EUR][1000 genomes]
rs73228040	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73230052	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs73230077	0.86[EUR][1000 genomes]
rs73230078	0.86[EUR][1000 genomes]
rs73230095	0.84[EUR][1000 genomes]
rs73231917	0.82[EUR][1000 genomes]
rs7636806	0.94[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs7646563	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7646723	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs923001	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv460861	chr3:136222954-136425600	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv591851	chr3:136222954-136425600	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv1008866	chr3:136364511-136427790	Weak transcription Enhancers Genic enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
4	nsv877529	chr3:136364511-136487559	ZNF genes & repeats Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs68018658	IL20RB	cis	Nerve Tibial	GTEx

Chromatin state (count:78 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:136365000-136396400	Weak transcription	Gastric	stomach
2	chr3:136376600-136392200	Weak transcription	Placenta	Placenta
3	chr3:136378600-136393600	Weak transcription	Fetal Lung	lung
4	chr3:136378600-136394000	Weak transcription	Adipose Nuclei	Adipose
5	chr3:136379200-136394000	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr3:136379600-136391800	Weak transcription	Cortex derived primary cultured neurospheres	brain
7	chr3:136381600-136392400	Weak transcription	Small Intestine	intestine
8	chr3:136381800-136410800	Weak transcription	Psoas Muscle	Psoas
9	chr3:136382600-136394200	Weak transcription	Fetal Heart	heart
10	chr3:136383000-136393200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
11	chr3:136383400-136394800	Weak transcription	Ovary	ovary
12	chr3:136383600-136395800	Weak transcription	Colon Smooth Muscle	Colon
13	chr3:136383800-136391800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
14	chr3:136384000-136392400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr3:136384200-136392000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr3:136384200-136392000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
17	chr3:136384200-136393200	Weak transcription	Brain Anterior Caudate	brain
18	chr3:136384200-136393800	Weak transcription	Brain Substantia Nigra	brain
19	chr3:136384400-136392000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr3:136385200-136392000	Weak transcription	Rectal Mucosa Donor 31	rectum
21	chr3:136385200-136394000	Weak transcription	Primary T cells fromperipheralblood	blood
22	chr3:136385200-136398400	Weak transcription	Fetal Intestine Large	intestine
23	chr3:136385400-136392400	Weak transcription	Fetal Muscle Leg	muscle
24	chr3:136385400-136393800	Weak transcription	Stomach Mucosa	stomach
25	chr3:136385600-136394000	Weak transcription	Sigmoid Colon	Sigmoid Colon
26	chr3:136386200-136393600	Weak transcription	NHLF	lung
27	chr3:136386400-136393800	Weak transcription	Duodenum Mucosa	Duodenum
28	chr3:136386400-136412800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr3:136386600-136394000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr3:136387000-136394800	Weak transcription	K562	blood
31	chr3:136387000-136396400	Weak transcription	Esophagus	oesophagus
32	chr3:136387200-136412400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr3:136387600-136393200	Weak transcription	Lung	lung
34	chr3:136387800-136397800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr3:136388000-136393200	Weak transcription	Primary B cells from cord blood	blood
36	chr3:136388000-136393200	Weak transcription	GM12878-XiMat	blood
37	chr3:136388200-136392200	Weak transcription	Fetal Thymus	thymus
38	chr3:136388200-136393600	Weak transcription	Primary B cells from peripheral blood	blood
39	chr3:136388400-136392000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr3:136388400-136392200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr3:136388400-136392200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr3:136389200-136393200	Weak transcription	Monocytes-CD14+_RO01746	blood
43	chr3:136389600-136394000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
44	chr3:136389600-136395400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
45	chr3:136390000-136393200	Weak transcription	Primary neutrophils fromperipheralblood	blood
46	chr3:136390200-136413000	Weak transcription	Pancreas	Pancrea
47	chr3:136390400-136392000	Enhancers	NHDF-Ad	bronchial
48	chr3:136390600-136392000	Enhancers	Duodenum Smooth Muscle	Duodenum
49	chr3:136390600-136392400	Enhancers	Pancreatic Islets	Pancreatic Islet
50	chr3:136390600-136392400	Weak transcription	Fetal Muscle Trunk	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links