Variant report

Variant	rs1539872
Chromosome Location	chr18:45425478-45425479
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	TCF12	chr18:45424872-45425587	A549	lung:	n/a	n/a
2	NFIC	chr18:45424880-45425674	ECC-1	luminal epithelium:	n/a	chr18:45425215-45425232 chr18:45425215-45425231
3	NFIC	chr18:45424897-45425478	SK-N-SH	brain:	n/a	chr18:45425215-45425232 chr18:45425215-45425231
4	SP1	chr18:45425055-45425483	A549	lung:	n/a	n/a
5	RAD21	chr18:45425369-45425849	H1-hESC	embryonic stem cell:	n/a	n/a
6	MAFK	chr18:45425464-45425947	H1-hESC	embryonic stem cell:	n/a	n/a
7	RAD21	chr18:45425460-45425924	MCF-7	breast:	n/a	n/a
8	RAD21	chr18:45425428-45425872	ECC-1	luminal epithelium:	n/a	n/a
9	CTCF	chr18:45425446-45425757	MCF-7	breast:	n/a	n/a
10	NFIC	chr18:45424919-45425528	ECC-1	luminal epithelium:	n/a	chr18:45425215-45425232 chr18:45425215-45425231
11	MYC	chr18:45425283-45425799	K562	blood:	n/a	chr18:45425707-45425718
12	RAD21	chr18:45425475-45425839	H1-hESC	embryonic stem cell:	n/a	n/a
13	CTCF	chr18:45425476-45425819	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr18:45423054..45427118-chr18:45456865..45459520,4	MCF-7	breast:
2	chr18:45425101..45428042-chr18:45452196..45454277,2	MCF-7	breast:
3	chr18:45424599..45427357-chr18:45454563..45456845,2	K562	blood:
4	chr18:45422809..45427886-chr18:45455832..45459212,8	MCF-7	breast:

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

Extended variants
information (count: 96 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:95)

rs_ID	r²[population]
rs10432199	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10502890	0.85[CEU][hapmap]
rs10853560	1.00[CEU][hapmap];0.82[JPT][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11082638	1.00[ASW][hapmap];1.00[CEU][hapmap];0.97[GIH][hapmap];0.82[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.93[TSI][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11082639	0.93[CEU][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11082641	0.89[CEU][hapmap]
rs11874858	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12457664	0.85[CEU][hapmap]
rs12458238	0.96[CEU][hapmap];0.84[EUR][1000 genomes]
rs12604337	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12605333	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12956483	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12968107	1.00[CEU][hapmap];0.82[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12968493	0.96[CEU][hapmap];0.83[TSI][hapmap];0.83[EUR][1000 genomes]
rs12969725	0.96[CEU][hapmap];0.80[TSI][hapmap];0.82[EUR][1000 genomes]
rs1539871	0.91[CHB][hapmap];0.84[CHD][hapmap];0.89[GIH][hapmap];0.90[JPT][hapmap];0.85[MEX][hapmap];0.91[ASN][1000 genomes]
rs1573362	0.85[CEU][hapmap]
rs1573363	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1613672	0.96[CEU][hapmap];0.82[JPT][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1631576	0.96[CEU][hapmap];0.94[GIH][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17741998	1.00[CEU][hapmap];0.82[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1787176	0.96[CEU][hapmap];0.82[JPT][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1787185	0.92[CEU][hapmap];1.00[JPT][hapmap]
rs1787186	0.92[CEU][hapmap]
rs1787193	0.96[CEU][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1787194	0.96[CEU][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1787195	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1787196	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1787197	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1787198	0.83[EUR][1000 genomes]
rs1792653	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1792655	0.96[CEU][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1792667	0.83[EUR][1000 genomes]
rs1792668	0.96[CEU][hapmap];0.83[TSI][hapmap];0.83[EUR][1000 genomes]
rs1792669	1.00[CEU][hapmap];0.82[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1792670	1.00[CEU][hapmap];0.94[GIH][hapmap];0.82[JPT][hapmap];0.90[MEX][hapmap];0.95[TSI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1792671	0.96[CEU][hapmap];1.00[JPT][hapmap]
rs1792672	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1792674	0.92[CEU][hapmap];0.83[TSI][hapmap];0.81[EUR][1000 genomes]
rs1792675	0.96[CEU][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1792679	0.92[CEU][hapmap];1.00[JPT][hapmap]
rs1792681	0.88[CEU][hapmap];0.94[GIH][hapmap];0.90[JPT][hapmap];0.89[MEX][hapmap];0.93[TSI][hapmap]
rs1792682	0.92[CEU][hapmap];1.00[JPT][hapmap]
rs1792683	0.89[CEU][hapmap];0.94[GIH][hapmap];0.82[JPT][hapmap];0.84[MEX][hapmap];0.81[MKK][hapmap];0.98[TSI][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1792686	0.96[CEU][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.87[TSI][hapmap]
rs1792687	0.92[CEU][hapmap];0.80[TSI][hapmap];0.83[EUR][1000 genomes]
rs1981	0.92[CEU][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.95[TSI][hapmap]
rs2000708	0.89[CEU][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2000709	0.85[CEU][hapmap];0.83[CHB][hapmap];0.90[JPT][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2012555	1.00[CEU][hapmap];0.94[GIH][hapmap];0.82[JPT][hapmap];0.89[TSI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2096932	0.82[JPT][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2096933	0.89[CEU][hapmap];0.82[JPT][hapmap];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs28548478	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs35710478	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3813068	0.83[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.98[TSI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4939672	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4940102	0.96[CEU][hapmap];0.81[EUR][1000 genomes]
rs4940109	0.89[CEU][hapmap];0.83[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.95[MEX][hapmap];0.87[TSI][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4940110	0.89[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4940120	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4940127	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61513611	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62086544	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6507790	0.93[CEU][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.91[TSI][hapmap];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6507791	1.00[CEU][hapmap];0.82[JPT][hapmap]
rs7228393	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7231538	1.00[CEU][hapmap];0.82[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7232764	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7232893	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7233129	1.00[CEU][hapmap];0.82[JPT][hapmap];0.91[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7236177	1.00[CEU][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7237544	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7243502	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs729112	1.00[CEU][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs747952	1.00[CEU][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs747953	1.00[CEU][hapmap];0.82[JPT][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs765213	0.85[CEU][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs8084915	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs8095519	1.00[ASW][hapmap];0.89[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.91[TSI][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs8097580	1.00[CEU][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs8097912	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8097925	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs8099127	1.00[CEU][hapmap];0.82[JPT][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs8099681	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs948600	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs948601	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs948602	0.96[CEU][hapmap]
rs948603	1.00[CEU][hapmap];0.82[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs948604	0.89[CEU][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9946556	0.96[CEU][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9950207	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9955626	1.00[CEU][hapmap];0.82[JPT][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9961652	0.82[ASN][1000 genomes]
rs9966637	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9966964	0.96[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[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	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1539872	SMAD2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:45397000-45430600	Weak transcription	Brain Angular Gyrus	brain
2	chr18:45400400-45432200	Weak transcription	Ovary	ovary
3	chr18:45401200-45426000	Weak transcription	Brain Cingulate Gyrus	brain
4	chr18:45409200-45426400	Weak transcription	Fetal Kidney	kidney
5	chr18:45410800-45425800	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr18:45410800-45428000	Weak transcription	Aorta	Aorta
7	chr18:45415200-45426000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
8	chr18:45417400-45426600	Weak transcription	Cortex derived primary cultured neurospheres	brain
9	chr18:45418200-45428400	Weak transcription	Thymus	Thymus
10	chr18:45419600-45428000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr18:45420000-45426200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
12	chr18:45420600-45427000	Weak transcription	Primary neutrophils fromperipheralblood	blood
13	chr18:45420800-45433000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr18:45420800-45439600	Weak transcription	Muscle Satellite Cultured Cells	--
15	chr18:45421000-45425800	Genic enhancers	Hela-S3	cervix
16	chr18:45421000-45430600	Weak transcription	Right Ventricle	heart
17	chr18:45421200-45436800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr18:45421600-45425800	Weak transcription	Brain Germinal Matrix	brain
19	chr18:45421800-45426600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
20	chr18:45421800-45428000	Weak transcription	Rectal Mucosa Donor 31	rectum
21	chr18:45421800-45428400	Weak transcription	Psoas Muscle	Psoas
22	chr18:45421800-45430400	Weak transcription	Esophagus	oesophagus
23	chr18:45421800-45430600	Weak transcription	H9 Cell Line	embryonic stem cell
24	chr18:45421800-45437800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr18:45422200-45425800	Weak transcription	GM12878-XiMat	blood
26	chr18:45422200-45429200	Weak transcription	Stomach Smooth Muscle	stomach
27	chr18:45422200-45430600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr18:45422600-45425600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
29	chr18:45422600-45426000	Weak transcription	Fetal Muscle Leg	muscle
30	chr18:45422600-45426400	Weak transcription	Fetal Brain Female	brain
31	chr18:45423000-45430600	Weak transcription	NHLF	lung
32	chr18:45423000-45432800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr18:45423200-45425600	Enhancers	Primary T helper cells PMA-I stimulated	--
34	chr18:45423200-45425600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
35	chr18:45423200-45425600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr18:45423200-45425800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr18:45423200-45426400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
38	chr18:45423200-45426400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr18:45423200-45427600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
40	chr18:45423200-45428000	Weak transcription	Primary T cells fromperipheralblood	blood
41	chr18:45423200-45428000	Weak transcription	Fetal Thymus	thymus
42	chr18:45423200-45428000	Weak transcription	Sigmoid Colon	Sigmoid Colon
43	chr18:45423200-45428400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr18:45423200-45428400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
45	chr18:45423200-45428400	Weak transcription	Spleen	Spleen
46	chr18:45423200-45429000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr18:45423200-45429200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr18:45423200-45429200	Weak transcription	Right Atrium	heart
49	chr18:45423200-45429200	Weak transcription	Skeletal Muscle Female	skeletal muscle
50	chr18:45423200-45430000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links