Variant report

Variant	rs12969725
Chromosome Location	chr18:45441352-45441353
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr18:45439344..45444269-chr18:45455068..45458587,5	K562	blood:
2	chr18:45440386..45443120-chr18:45446937..45449451,2	MCF-7	breast:
3	chr18:45439039..45441634-chr18:45452955..45455422,2	MCF-7	breast:
4	chr18:45431906..45433544-chr18:45439768..45441940,2	MCF-7	breast:
5	chr18:45439535..45445304-chr18:45455068..45459362,9	K562	blood:
6	chr18:45440670..45442541-chr18:45446243..45448520,2	K562	blood:

Variant related genes	Relation type
ENSG00000175387	Chromatin interaction

Extended variants
information (count: 85 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:84)

rs_ID	r²[population]
rs10445485	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10502890	1.00[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10853560	0.96[CEU][hapmap];0.83[EUR][1000 genomes]
rs11082638	0.96[CEU][hapmap];0.83[EUR][1000 genomes]
rs11082639	0.89[CEU][hapmap]
rs11082641	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11659463	0.83[AFR][1000 genomes]
rs12457664	1.00[ASW][hapmap];0.89[CEU][hapmap];0.87[CHD][hapmap];0.98[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12458238	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12968107	0.96[CEU][hapmap];0.82[EUR][1000 genomes]
rs12968493	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.98[MKK][hapmap];0.98[TSI][hapmap];0.91[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1539871	0.81[ASW][hapmap];0.89[LWK][hapmap]
rs1539872	0.96[CEU][hapmap];0.80[TSI][hapmap];0.82[EUR][1000 genomes]
rs1573362	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1573363	0.96[CEU][hapmap];0.83[EUR][1000 genomes]
rs1613672	0.93[CEU][hapmap]
rs1631576	0.92[CEU][hapmap];0.83[TSI][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	0.93[ASW][hapmap];0.96[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];0.97[LWK][hapmap];0.89[MKK][hapmap];0.93[TSI][hapmap];0.86[YRI][hapmap]
rs1787193	0.93[CEU][hapmap]
rs1787194	0.93[CEU][hapmap]
rs1787196	0.84[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs1787197	0.82[EUR][1000 genomes]
rs1787198	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1787199	0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.98[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs1792655	0.93[CEU][hapmap]
rs1792658	0.83[LWK][hapmap];0.83[YRI][hapmap]
rs1792666	0.91[CHB][hapmap];0.90[JPT][hapmap];0.95[YRI][hapmap]
rs1792667	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1792668	0.93[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.98[MKK][hapmap];0.98[TSI][hapmap];0.95[YRI][hapmap];0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1792669	0.96[CEU][hapmap];0.83[EUR][1000 genomes]
rs1792670	0.96[CEU][hapmap];0.85[TSI][hapmap];0.83[EUR][1000 genomes]
rs1792671	0.93[CEU][hapmap]
rs1792674	0.87[ASW][hapmap];0.96[CEU][hapmap];0.85[CHD][hapmap];0.98[GIH][hapmap];0.81[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];0.95[YRI][hapmap];0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[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];0.82[TSI][hapmap]
rs1792684	0.95[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];0.90[JPT][hapmap];0.92[LWK][hapmap];0.96[MKK][hapmap];0.81[TSI][hapmap];0.95[YRI][hapmap]
rs1792686	0.81[ASW][hapmap];0.92[CEU][hapmap];0.94[LWK][hapmap];0.89[TSI][hapmap];0.95[YRI][hapmap]
rs1792687	0.93[ASW][hapmap];0.96[CEU][hapmap];0.87[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.98[MKK][hapmap];0.95[TSI][hapmap];0.95[YRI][hapmap];0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1792689	1.00[YRI][hapmap]
rs1942158	0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs1981	0.89[CEU][hapmap];0.80[TSI][hapmap]
rs2000708	0.85[CEU][hapmap]
rs2000709	0.81[CEU][hapmap]
rs2012555	0.96[CEU][hapmap];0.83[LWK][hapmap];0.91[TSI][hapmap];0.83[YRI][hapmap];0.83[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs2096932	0.82[EUR][1000 genomes]
rs2096933	0.85[CEU][hapmap]
rs3813068	0.92[CEU][hapmap];0.83[TSI][hapmap];0.82[EUR][1000 genomes]
rs4940102	1.00[CEU][hapmap];0.90[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4940109	0.85[CEU][hapmap]
rs4940110	0.85[CEU][hapmap]
rs4940120	0.82[EUR][1000 genomes]
rs57620563	0.96[AFR][1000 genomes]
rs61513611	0.86[EUR][1000 genomes]
rs6507790	0.89[CEU][hapmap]
rs6507791	0.96[CEU][hapmap]
rs7228393	0.88[CEU][hapmap]
rs7231538	0.96[CEU][hapmap];0.83[EUR][1000 genomes]
rs7232893	0.82[EUR][1000 genomes]
rs7233129	0.96[CEU][hapmap];0.82[EUR][1000 genomes]
rs7236177	0.96[CEU][hapmap];0.80[TSI][hapmap];0.82[EUR][1000 genomes]
rs7237544	0.82[EUR][1000 genomes]
rs729112	0.96[CEU][hapmap];0.83[TSI][hapmap];0.82[EUR][1000 genomes]
rs747952	0.96[CEU][hapmap];0.82[EUR][1000 genomes]
rs747953	0.96[CEU][hapmap];0.82[EUR][1000 genomes]
rs765213	0.81[CEU][hapmap]
rs8084915	0.82[EUR][1000 genomes]
rs8095519	0.85[CEU][hapmap]
rs8097580	0.95[CEU][hapmap];0.82[EUR][1000 genomes]
rs8097912	0.96[CEU][hapmap];0.82[EUR][1000 genomes]
rs8099127	0.96[CEU][hapmap];0.82[EUR][1000 genomes]
rs948602	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs948603	0.96[CEU][hapmap];0.82[EUR][1000 genomes]
rs948604	0.85[CEU][hapmap]
rs9946556	0.93[CEU][hapmap]
rs9950207	0.82[EUR][1000 genomes]
rs9955626	0.96[CEU][hapmap];0.86[EUR][1000 genomes]
rs9966637	0.83[EUR][1000 genomes]
rs9966964	0.93[CEU][hapmap];0.83[TSI][hapmap];0.81[EUR][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

No data

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:45423200-45451400	Weak transcription	Rectal Mucosa Donor 29	rectum
2	chr18:45431000-45442800	Weak transcription	Lung	lung
3	chr18:45433200-45455000	Weak transcription	Fetal Stomach	stomach
4	chr18:45433200-45455400	Weak transcription	Fetal Brain Male	brain
5	chr18:45433400-45442800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr18:45433400-45442800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr18:45433400-45446400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr18:45433400-45452200	Weak transcription	Fetal Lung	lung
9	chr18:45433600-45446000	Weak transcription	Placenta	Placenta
10	chr18:45434000-45442000	Weak transcription	HSMM	muscle
11	chr18:45434000-45446600	Weak transcription	Primary B cells from cord blood	blood
12	chr18:45434000-45454600	Weak transcription	Primary B cells from peripheral blood	blood
13	chr18:45435000-45442200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr18:45435400-45452400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr18:45435600-45444400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr18:45435600-45455800	Weak transcription	Fetal Muscle Trunk	muscle
17	chr18:45436600-45441600	Weak transcription	NHDF-Ad	bronchial
18	chr18:45436800-45442000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
19	chr18:45437200-45444800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr18:45437600-45442400	Enhancers	Primary T helper cells fromperipheralblood	blood
21	chr18:45437600-45442600	Enhancers	Colon Smooth Muscle	Colon
22	chr18:45437600-45442800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
23	chr18:45438000-45442000	Enhancers	Rectal Smooth Muscle	rectum
24	chr18:45438000-45442400	Enhancers	Duodenum Smooth Muscle	Duodenum
25	chr18:45438000-45444200	Enhancers	iPS-15b Cell Line	embryonic stem cell
26	chr18:45438200-45442400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr18:45438400-45444800	Weak transcription	Primary neutrophils fromperipheralblood	blood
28	chr18:45438600-45454600	Enhancers	Primary T helper cells PMA-I stimulated	--
29	chr18:45438800-45442200	Enhancers	Skeletal Muscle Male	skeletal muscle
30	chr18:45438800-45442400	Enhancers	Primary T killer memory cells from peripheral blood	blood
31	chr18:45438800-45442600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
32	chr18:45438800-45446000	Weak transcription	Dnd41	blood
33	chr18:45438800-45453400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr18:45439000-45441600	Weak transcription	HUES6 Cell Line	embryonic stem cell
35	chr18:45439000-45441800	Enhancers	Primary T cells from cord blood	blood
36	chr18:45439000-45442800	Weak transcription	Ovary	ovary
37	chr18:45439000-45443400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
38	chr18:45439000-45443800	Enhancers	K562	blood
39	chr18:45439000-45444000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr18:45439000-45444400	Weak transcription	H9 Cell Line	embryonic stem cell
41	chr18:45439000-45444600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr18:45439000-45444800	Weak transcription	Small Intestine	intestine
43	chr18:45439000-45445000	Enhancers	A549	lung
44	chr18:45439000-45445200	Weak transcription	Thymus	Thymus
45	chr18:45439000-45452200	Weak transcription	Sigmoid Colon	Sigmoid Colon
46	chr18:45439000-45452800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr18:45439000-45452800	Weak transcription	Aorta	Aorta
48	chr18:45439000-45456200	Weak transcription	Esophagus	oesophagus
49	chr18:45439000-45456200	Weak transcription	Spleen	Spleen
50	chr18:45439200-45444400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links