Variant report

Variant	rs4940102
Chromosome Location	chr18:45454829-45454830
allele	A/C
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	POLR2A	chr18:45454367-45459190	MCF10A-Er-Src	breast:	n/a	n/a
2	POLR2A	chr18:45454672-45458824	Hela-S3	cervix:	n/a	n/a
3	IRF1	chr18:45454550-45454990	K562	blood:	n/a	chr18:45454627-45454641 chr18:45454809-45454819 chr18:45454805-45454819 chr18:45454809-45454823 chr18:45454663-45454675
4	POLR2A	chr18:45454444-45454983	GM12878	blood:	n/a	n/a
5	TBP	chr18:45454756-45455566	Hela-S3	cervix:	n/a	n/a
6	FOXA1	chr18:45454725-45455208	HepG2	liver:	n/a	n/a
7	IRF1	chr18:45454604-45456466	K562	blood:	n/a	chr18:45455005-45455012 chr18:45454627-45454641 chr18:45455862-45455869 chr18:45454809-45454819 chr18:45454805-45454819 chr18:45454809-45454823 chr18:45455069-45455081 chr18:45456026-45456038 chr18:45454663-45454675
8	FOS	chr18:45454819-45455240	MCF10A-Er-Src	breast:	n/a	n/a
9	POLR2A	chr18:45454445-45455407	MCF10A-Er-Src	breast:	n/a	n/a
10	STAT3	chr18:45454800-45454958	MCF10A-Er-Src	breast:	n/a	n/a
11	RUNX3	chr18:45454821-45455224	GM12878	blood:	n/a	n/a
12	EP300	chr18:45454681-45454955	K562	blood:	n/a	chr18:45454804-45454818

No.	Distal block	Cell Line	Cell type
1	chr18:45370062..45371817-chr18:45453252..45455227,2	MCF-7	breast:
2	chr18:45445551..45451271-chr18:45453158..45456977,7	K562	blood:
3	chr18:45412211..45417305-chr18:45454331..45458060,5	MCF-7	breast:
4	chr18:45412744..45415150-chr18:45452720..45455335,2	MCF-7	breast:
5	chr18:45450692..45455196-chr18:45455930..45459309,6	MCF-7	breast:
6	chr18:45439039..45441634-chr18:45452955..45455422,2	MCF-7	breast:
7	chr18:45452201..45455106-chr18:45476820..45479374,2	MCF-7	breast:

Variant related genes	Relation type
SMAD2	TF binding region
ENSG00000175387	Chromatin interaction

Extended variants
information (count: 81 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs10445485	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10502890	0.89[CEU][hapmap];0.86[JPT][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10853560	0.96[CEU][hapmap];0.81[EUR][1000 genomes]
rs11082638	0.96[CEU][hapmap];0.81[EUR][1000 genomes]
rs11082639	0.86[CEU][hapmap]
rs11082641	0.90[CEU][hapmap];0.91[JPT][hapmap];0.81[AMR][1000 genomes]
rs12457664	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12458238	1.00[CEU][hapmap];0.91[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12968107	0.96[CEU][hapmap];0.82[EUR][1000 genomes]
rs12968493	1.00[CEU][hapmap];0.90[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12969725	1.00[CEU][hapmap];0.90[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1539872	0.96[CEU][hapmap];0.81[EUR][1000 genomes]
rs1573362	0.86[CEU][hapmap];0.91[JPT][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1573363	0.96[CEU][hapmap];0.83[EUR][1000 genomes]
rs1613672	0.93[CEU][hapmap]
rs1631576	0.92[CEU][hapmap];0.82[EUR][1000 genomes]
rs17741998	0.96[CEU][hapmap];0.82[EUR][1000 genomes]
rs1787176	0.93[CEU][hapmap];0.80[EUR][1000 genomes]
rs1787185	0.89[CEU][hapmap]
rs1787186	0.96[CEU][hapmap];1.00[JPT][hapmap]
rs1787193	0.93[CEU][hapmap]
rs1787194	0.93[CEU][hapmap]
rs1787196	0.86[EUR][1000 genomes]
rs1787197	0.81[EUR][1000 genomes]
rs1787198	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1787199	0.91[JPT][hapmap]
rs1792655	0.93[CEU][hapmap]
rs1792666	1.00[JPT][hapmap]
rs1792667	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1792668	1.00[CEU][hapmap];0.90[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1792669	0.96[CEU][hapmap];0.82[EUR][1000 genomes]
rs1792670	0.96[CEU][hapmap];0.82[EUR][1000 genomes]
rs1792671	0.93[CEU][hapmap]
rs1792674	0.96[CEU][hapmap];0.90[JPT][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1792675	0.93[CEU][hapmap]
rs1792679	0.89[CEU][hapmap]
rs1792681	0.85[CEU][hapmap]
rs1792682	0.89[CEU][hapmap]
rs1792683	0.85[CEU][hapmap]
rs1792684	1.00[JPT][hapmap]
rs1792686	0.92[CEU][hapmap]
rs1792687	0.96[CEU][hapmap];0.90[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1942158	0.91[JPT][hapmap]
rs1981	0.89[CEU][hapmap]
rs2000708	0.82[CEU][hapmap]
rs2012555	0.96[CEU][hapmap];0.86[EUR][1000 genomes]
rs2096932	0.82[EUR][1000 genomes]
rs2096933	0.82[CEU][hapmap]
rs3813068	0.92[CEU][hapmap];0.81[EUR][1000 genomes]
rs4940109	0.85[CEU][hapmap]
rs4940110	0.82[CEU][hapmap]
rs4940120	0.83[EUR][1000 genomes]
rs4940127	0.81[EUR][1000 genomes]
rs57620563	0.98[ASN][1000 genomes]
rs61513611	0.84[EUR][1000 genomes]
rs6507790	0.89[CEU][hapmap]
rs6507791	0.96[CEU][hapmap]
rs7228393	0.88[CEU][hapmap]
rs7231538	0.96[CEU][hapmap];0.82[EUR][1000 genomes]
rs7232893	0.81[EUR][1000 genomes]
rs7233129	0.96[CEU][hapmap];0.82[EUR][1000 genomes]
rs7236177	0.96[CEU][hapmap];0.81[EUR][1000 genomes]
rs7237544	0.81[EUR][1000 genomes]
rs729112	0.96[CEU][hapmap];0.82[EUR][1000 genomes]
rs747952	0.96[CEU][hapmap];0.81[EUR][1000 genomes]
rs747953	0.96[CEU][hapmap];0.81[EUR][1000 genomes]
rs8084915	0.81[EUR][1000 genomes]
rs8095519	0.85[CEU][hapmap]
rs8097580	0.96[CEU][hapmap];0.81[EUR][1000 genomes]
rs8097912	0.96[CEU][hapmap];0.81[EUR][1000 genomes]
rs8099127	0.96[CEU][hapmap];0.81[EUR][1000 genomes]
rs948602	1.00[CEU][hapmap];0.91[JPT][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs948603	0.96[CEU][hapmap];0.81[EUR][1000 genomes]
rs948604	0.85[CEU][hapmap]
rs9946556	0.93[CEU][hapmap]
rs9950207	0.81[EUR][1000 genomes]
rs9955626	0.96[CEU][hapmap];0.85[EUR][1000 genomes]
rs9966637	0.82[EUR][1000 genomes]
rs9966964	0.93[CEU][hapmap];0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4940102	SMAD2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:45433200-45455000	Weak transcription	Fetal Stomach	stomach
2	chr18:45433200-45455400	Weak transcription	Fetal Brain Male	brain
3	chr18:45435600-45455800	Weak transcription	Fetal Muscle Trunk	muscle
4	chr18:45439000-45456200	Weak transcription	Esophagus	oesophagus
5	chr18:45439000-45456200	Weak transcription	Spleen	Spleen
6	chr18:45439600-45455400	Weak transcription	Fetal Muscle Leg	muscle
7	chr18:45439800-45456200	Weak transcription	Pancreas	Pancrea
8	chr18:45442400-45455000	Weak transcription	HSMM	muscle
9	chr18:45443000-45456000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr18:45443600-45455000	Weak transcription	Osteobl	bone
11	chr18:45444800-45456000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr18:45444800-45456000	Weak transcription	Lung	lung
13	chr18:45446000-45455400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
14	chr18:45446200-45455800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr18:45447600-45456000	Weak transcription	Left Ventricle	heart
16	chr18:45450000-45456200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr18:45450200-45455200	Weak transcription	Right Ventricle	heart
18	chr18:45450800-45455000	Enhancers	Primary T killer memory cells from peripheral blood	blood
19	chr18:45451000-45455600	Enhancers	Primary T helper naive cells from peripheral blood	blood
20	chr18:45451000-45455600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
21	chr18:45451600-45455000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
22	chr18:45451600-45455200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
23	chr18:45451600-45456000	Enhancers	Fetal Heart	heart
24	chr18:45452000-45456000	Enhancers	Brain Hippocampus Middle	brain
25	chr18:45452200-45455000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
26	chr18:45452200-45455000	Enhancers	Skeletal Muscle Female	skeletal muscle
27	chr18:45452200-45456000	Enhancers	Brain Substantia Nigra	brain
28	chr18:45452400-45455000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr18:45452400-45455000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr18:45452400-45455200	Enhancers	Small Intestine	intestine
31	chr18:45452400-45455800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr18:45452400-45455800	Enhancers	Brain Anterior Caudate	brain
33	chr18:45452400-45455800	Enhancers	Fetal Intestine Small	intestine
34	chr18:45452400-45456000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
35	chr18:45452600-45456000	Enhancers	Brain Inferior Temporal Lobe	brain
36	chr18:45452800-45456000	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
37	chr18:45453000-45455000	Enhancers	Primary hematopoietic stem cells	blood
38	chr18:45453000-45455800	Enhancers	Brain Angular Gyrus	brain
39	chr18:45453400-45455800	Weak transcription	Aorta	Aorta
40	chr18:45453400-45455800	Enhancers	Liver	Liver
41	chr18:45453600-45456000	Enhancers	Primary monocytes fromperipheralblood	blood
42	chr18:45453600-45458200	Active TSS	GM12878-XiMat	blood
43	chr18:45453800-45455200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr18:45453800-45455800	Weak transcription	Psoas Muscle	Psoas
45	chr18:45453800-45456200	Weak transcription	Gastric	stomach
46	chr18:45454000-45456000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr18:45454000-45456000	Weak transcription	Sigmoid Colon	Sigmoid Colon
48	chr18:45454200-45455000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr18:45454200-45455000	Enhancers	NH-A	brain
50	chr18:45454200-45455200	Enhancers	Cortex derived primary cultured neurospheres	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links