Variant report

Variant	rs12472524
Chromosome Location	chr2:152972696-152972697
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:152972562..152974941-chr2:152975628..152977362,2	MCF-7	breast:
2	chr2:152893247..152893922-chr2:152972233..152973059,2	MCF-7	breast:
3	chr2:152904299..152905163-chr2:152971928..152972728,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-FMNL2-4	chr2:152972498-152972944	NONHSAT074973

Extended variants
information (count: 70 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs10177222	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10187630	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10203659	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10469642	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10497095	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10497097	0.90[CEU][hapmap];0.87[CHB][hapmap];0.93[JPT][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10803946	0.94[CEU][hapmap]
rs10930923	0.83[AMR][1000 genomes]
rs10930939	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10930959	0.90[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1133478	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11694120	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11884659	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11893841	0.95[CEU][hapmap];0.93[CHB][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12328733	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12468532	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12476550	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12612557	0.89[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12613984	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12615156	0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12621378	0.85[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.94[YRI][hapmap];0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12622092	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12623355	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12693270	0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12693271	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13003423	0.90[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13009614	0.85[AMR][1000 genomes]
rs13424583	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13426474	0.80[AMR][1000 genomes]
rs2002247	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34233450	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35155943	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35717822	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3768648	0.94[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3768649	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3768651	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3806464	0.84[CEU][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4255959	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4368329	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4473376	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4505521	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4611639	0.85[CEU][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4664080	0.84[ASN][1000 genomes]
rs4664084	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4664085	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4664089	0.94[CEU][hapmap]
rs4664530	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4664531	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs4664532	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4664535	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4664537	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62176474	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62176476	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62176478	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62176479	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6650779	0.89[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6720552	0.84[CEU][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs71417204	0.82[ASN][1000 genomes]
rs7419567	0.83[AMR][1000 genomes]
rs7420277	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7572616	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7588906	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9917198	0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1005746	chr2:152361972-153059840	Strong transcription Weak transcription Bivalent/Poised TSS Enhancers Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
2	nsv535984	chr2:152361972-153059840	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	esv3693431	chr2:152683731-152981827	Enhancers Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
4	nsv875287	chr2:152714680-153110573	Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
5	nsv875288	chr2:152716628-153183646	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
6	nsv875289	chr2:152720030-153183646	Enhancers Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
7	esv1847028	chr2:152863856-153045036	Weak transcription Active TSS Bivalent/Poised TSS Strong transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:152956200-152978600	Weak transcription	Aorta	Aorta
2	chr2:152957200-152979400	Weak transcription	Rectal Smooth Muscle	rectum
3	chr2:152963000-152976000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr2:152964400-152977000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
5	chr2:152966200-152976000	Weak transcription	Primary B cells from cord blood	blood
6	chr2:152966600-152975800	Weak transcription	Placenta	Placenta
7	chr2:152967800-152976000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr2:152968000-152975600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr2:152968000-152975800	Weak transcription	HUES48 Cell Line	embryonic stem cell
10	chr2:152968000-152995800	Weak transcription	HSMMtube	muscle
11	chr2:152968800-152975800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
12	chr2:152969200-152978600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr2:152969400-152989000	Weak transcription	HepG2	liver
14	chr2:152970000-152977000	Weak transcription	Fetal Intestine Small	intestine
15	chr2:152970000-152977000	Weak transcription	Fetal Stomach	stomach
16	chr2:152970000-152977200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
17	chr2:152970000-152990800	Weak transcription	Stomach Mucosa	stomach
18	chr2:152970200-152977000	Weak transcription	Ovary	ovary
19	chr2:152970200-153003000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
20	chr2:152970600-152975800	Weak transcription	Duodenum Mucosa	Duodenum
21	chr2:152970600-152977000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
22	chr2:152970600-152977800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr2:152970800-152975800	Weak transcription	Primary T cells fromperipheralblood	blood
24	chr2:152970800-152975800	Weak transcription	Liver	Liver
25	chr2:152970800-152975800	Weak transcription	Duodenum Smooth Muscle	Duodenum
26	chr2:152970800-152976200	Weak transcription	NH-A	brain
27	chr2:152970800-152981400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr2:152971000-152976000	Weak transcription	Primary T helper cells fromperipheralblood	blood
29	chr2:152971000-152976000	Weak transcription	Fetal Muscle Leg	muscle
30	chr2:152971000-152976600	Weak transcription	Rectal Mucosa Donor 29	rectum
31	chr2:152971000-152977000	Weak transcription	Thymus	Thymus
32	chr2:152971000-152978400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr2:152971200-152975600	Weak transcription	Primary neutrophils fromperipheralblood	blood
34	chr2:152971200-152975800	Weak transcription	Skeletal Muscle Female	skeletal muscle
35	chr2:152971200-152976000	Weak transcription	Adipose Nuclei	Adipose
36	chr2:152971200-152976600	Weak transcription	Dnd41	blood
37	chr2:152971200-152977000	Weak transcription	Lung	lung
38	chr2:152971200-153008400	Weak transcription	Esophagus	oesophagus
39	chr2:152971400-152975200	Weak transcription	Primary monocytes fromperipheralblood	blood
40	chr2:152971400-153002200	Weak transcription	Brain Anterior Caudate	brain
41	chr2:152971800-152975800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr2:152971800-152977600	Weak transcription	Fetal Muscle Trunk	muscle
43	chr2:152971800-152980000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr2:152972000-152976000	Weak transcription	Brain Substantia Nigra	brain
45	chr2:152972000-152978600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr2:152972200-152973000	Strong transcription	Monocytes-CD14+_RO01746	blood
47	chr2:152972200-152975800	Weak transcription	Brain Angular Gyrus	brain
48	chr2:152972400-152972800	Enhancers	Fetal Heart	heart
49	chr2:152972400-152974000	Strong transcription	Primary T cells from cord blood	blood
50	chr2:152972400-152975200	Weak transcription	NHDF-Ad	bronchial

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links