Variant report

Variant	rs4940120
Chromosome Location	chr18:45463403-45463404
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr18:45462473..45465450-chr18:45470431..45471984,2	MCF-7	breast:
2	chr18:45455293..45460284-chr18:45461737..45465980,6	K562	blood:
3	chr18:45456285..45458398-chr18:45460688..45463962,5	MCF-7	breast:
4	chr18:45457328..45461000-chr18:45463318..45467382,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000175387	Chromatin interaction

Extended variants
information (count: 84 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:81)

rs_ID	r²[population]
rs10432199	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10853560	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11082638	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11082639	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11874858	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12458238	0.80[EUR][1000 genomes]
rs12604337	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12605333	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12956483	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12968107	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12968493	0.81[EUR][1000 genomes]
rs12969725	0.82[EUR][1000 genomes]
rs1539871	0.92[ASN][1000 genomes]
rs1539872	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1573363	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1613672	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1631576	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17741998	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1787176	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1787193	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1787194	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1787195	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1787196	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1787197	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1787198	0.81[EUR][1000 genomes]
rs1792653	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1792655	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1792667	0.81[EUR][1000 genomes]
rs1792668	0.81[EUR][1000 genomes]
rs1792669	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1792670	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1792672	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1792675	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1792683	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1792687	0.80[EUR][1000 genomes]
rs2000708	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2000709	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2012555	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2096932	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2096933	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs28548478	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs35710478	0.84[EUR][1000 genomes]
rs3813068	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4939672	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4940102	0.83[EUR][1000 genomes]
rs4940109	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4940110	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4940127	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61513611	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62086544	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6507790	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7228393	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7231538	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7232764	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7232893	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7233129	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7236177	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7237544	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7243502	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs729112	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs747952	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs747953	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs765213	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs8084915	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs8095519	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs8097580	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs8097912	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8097925	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs8099127	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs8099681	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs948600	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs948601	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs948603	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs948604	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9946556	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9947494	0.82[EUR][1000 genomes]
rs9950207	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9955626	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9961652	0.82[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs9966637	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9966964	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[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	nsv909614	chr18:45419421-45478490	Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Genic enhancers Strong transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	nsv909615	chr18:45452321-45493026	Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	esv3358262	chr18:45460344-45464204	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4940120	SMAD2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:45458800-45463600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
2	chr18:45459000-45464800	Weak transcription	Pancreas	Pancrea
3	chr18:45459600-45471600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr18:45459800-45464200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr18:45459800-45464600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr18:45461000-45463600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr18:45462200-45465000	Enhancers	Primary hematopoietic stem cells	blood
8	chr18:45462200-45465200	Enhancers	Fetal Thymus	thymus
9	chr18:45462400-45464200	Enhancers	Primary T cells from cord blood	blood
10	chr18:45462600-45465000	Enhancers	Thymus	Thymus
11	chr18:45463000-45463800	Enhancers	Monocytes-CD14+_RO01746	blood
12	chr18:45463000-45465200	Weak transcription	Right Atrium	heart
13	chr18:45463200-45463600	Enhancers	Primary T helper cells PMA-I stimulated	--
14	chr18:45463200-45463600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr18:45463200-45463800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
16	chr18:45463200-45463800	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
17	chr18:45463200-45463800	Enhancers	Hela-S3	cervix
18	chr18:45463200-45464000	Enhancers	Primary neutrophils fromperipheralblood	blood
19	chr18:45463200-45464000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr18:45463200-45465200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr18:45463400-45463600	Enhancers	Primary T cells fromperipheralblood	blood
22	chr18:45463400-45463600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
23	chr18:45463400-45463600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr18:45463400-45463800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
25	chr18:45463400-45463800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr18:45463400-45463800	Enhancers	Dnd41	blood
27	chr18:45463400-45464000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
28	chr18:45463400-45465200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links