Variant report

Variant	rs12228425
Chromosome Location	chr12:118742690-118742691
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:118740466..118742711-chr12:118813102..118814672,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000111707	Chromatin interaction
ENSG00000270482	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:80)

rs_ID	r²[population]
rs10850968	0.94[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap]
rs11068853	0.94[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap]
rs11068854	0.94[CHB][hapmap];0.84[JPT][hapmap];1.00[YRI][hapmap]
rs11068855	0.82[ASW][hapmap];0.94[CHB][hapmap];0.82[CHD][hapmap];0.96[GIH][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs11068856	0.94[CHB][hapmap];0.93[JPT][hapmap]
rs11068860	0.94[CHB][hapmap];0.82[CHD][hapmap];0.85[GIH][hapmap];0.92[JPT][hapmap];1.00[EUR][1000 genomes]
rs11068864	0.94[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11068865	0.94[CHB][hapmap];0.82[CHD][hapmap];0.92[GIH][hapmap];0.93[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs11068871	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11068872	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11068878	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11068880	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11068881	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11068883	0.84[ASN][1000 genomes]
rs11068887	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11068888	0.89[AFR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11068889	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11068891	0.94[CHB][hapmap];0.94[CHD][hapmap];0.87[JPT][hapmap];0.93[ASN][1000 genomes]
rs11068892	0.98[ASN][1000 genomes]
rs11068893	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11068896	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11068898	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11068899	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11068900	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs11068901	1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11068904	0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11068906	0.95[ASN][1000 genomes]
rs11068908	0.94[CHB][hapmap];0.94[CHD][hapmap];0.87[JPT][hapmap];0.95[ASN][1000 genomes]
rs11068909	1.00[CHB][hapmap];0.97[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11068914	1.00[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11068915	1.00[CHB][hapmap];0.86[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11068916	1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11068917	0.94[CHB][hapmap];0.94[CHD][hapmap];0.85[ASN][1000 genomes]
rs11068919	0.89[CHB][hapmap];0.84[ASN][1000 genomes]
rs11068920	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11068922	0.86[ASN][1000 genomes]
rs11068923	0.94[CHB][hapmap];0.94[CHD][hapmap];0.96[GIH][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11068924	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11068926	0.82[ASN][1000 genomes]
rs11068930	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11068933	0.94[CHB][hapmap];0.94[CHD][hapmap]
rs11068937	0.94[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs11068940	1.00[EUR][1000 genomes]
rs11068941	1.00[EUR][1000 genomes]
rs11068943	1.00[EUR][1000 genomes]
rs11068945	1.00[EUR][1000 genomes]
rs12227411	0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12227974	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12229607	0.86[CHB][hapmap];0.91[ASN][1000 genomes]
rs12230104	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12231358	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12231845	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16948250	0.89[CHB][hapmap];0.86[JPT][hapmap]
rs17586342	0.88[CHB][hapmap];0.82[CHD][hapmap]
rs17586582	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17619569	0.82[ASW][hapmap];0.94[CHB][hapmap];0.82[CHD][hapmap];0.96[GIH][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs17619702	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17619805	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17619932	0.94[CHB][hapmap];0.97[CHD][hapmap];0.88[ASN][1000 genomes]
rs2036314	0.82[ASN][1000 genomes]
rs2062520	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2271007	0.94[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2280711	0.88[CHB][hapmap];0.82[CHD][hapmap]
rs3741444	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4442583	0.82[ASN][1000 genomes]
rs61943365	0.89[ASN][1000 genomes]
rs61943369	0.82[ASN][1000 genomes]
rs61943370	0.80[ASN][1000 genomes]
rs61943371	0.80[ASN][1000 genomes]
rs61945207	0.89[ASN][1000 genomes]
rs61945219	0.93[ASN][1000 genomes]
rs6490177	0.85[ASN][1000 genomes]
rs7132582	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7136216	0.88[CHB][hapmap];0.82[CHD][hapmap]
rs7296216	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73222058	0.91[ASN][1000 genomes]
rs7963464	0.93[ASN][1000 genomes]
rs7974718	0.94[CHB][hapmap];0.87[JPT][hapmap];0.91[ASN][1000 genomes]
rs9888447	1.00[ASW][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9943792	0.82[ASW][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1053785	chr12:118490955-118874194	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
2	nsv1038224	chr12:118648415-118791388	Strong transcription Genic enhancers Weak transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv1040061	chr12:118648415-118800437	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv1053417	chr12:118688969-118808530	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12228425	SUDS3	cis	lymphoblastoid	seeQTL

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:118676000-118745200	Weak transcription	Duodenum Smooth Muscle	Duodenum
2	chr12:118693400-118745000	Weak transcription	Rectal Mucosa Donor 29	rectum
3	chr12:118702600-118744600	Weak transcription	Duodenum Mucosa	Duodenum
4	chr12:118712400-118745000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr12:118719200-118744400	Weak transcription	HSMM	muscle
6	chr12:118720800-118793600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr12:118722600-118745000	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr12:118726600-118746800	Weak transcription	Lung	lung
9	chr12:118728400-118744400	Weak transcription	NHLF	lung
10	chr12:118731200-118744400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr12:118732600-118744800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr12:118732800-118767600	Weak transcription	Primary T cells from cord blood	blood
13	chr12:118733400-118745000	Weak transcription	Primary T helper cells fromperipheralblood	blood
14	chr12:118735000-118744600	Weak transcription	Primary monocytes fromperipheralblood	blood
15	chr12:118735400-118744400	Weak transcription	Monocytes-CD14+_RO01746	blood
16	chr12:118735600-118745000	Weak transcription	Primary B cells from cord blood	blood
17	chr12:118736200-118746000	Weak transcription	Primary T cells fromperipheralblood	blood
18	chr12:118738000-118744600	Weak transcription	Fetal Intestine Small	intestine
19	chr12:118738000-118745000	Weak transcription	Small Intestine	intestine
20	chr12:118738200-118744400	Weak transcription	NH-A	brain
21	chr12:118738200-118745200	Weak transcription	Brain Hippocampus Middle	brain
22	chr12:118738200-118761800	Weak transcription	Fetal Lung	lung
23	chr12:118738400-118744800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr12:118738400-118745000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
25	chr12:118738600-118745200	Weak transcription	Brain Anterior Caudate	brain
26	chr12:118738600-118745600	Weak transcription	Brain Cingulate Gyrus	brain
27	chr12:118739000-118744800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
28	chr12:118739200-118749400	Weak transcription	Brain Angular Gyrus	brain
29	chr12:118739400-118743000	Enhancers	GM12878-XiMat	blood
30	chr12:118740000-118745000	Weak transcription	K562	blood
31	chr12:118740200-118744600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr12:118740200-118744800	Weak transcription	Primary B cells from peripheral blood	blood
33	chr12:118740200-118745000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
34	chr12:118740200-118745000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
35	chr12:118740200-118745000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr12:118740200-118745000	Weak transcription	Brain Inferior Temporal Lobe	brain
37	chr12:118740400-118743800	Weak transcription	Muscle Satellite Cultured Cells	--
38	chr12:118740400-118744200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr12:118740400-118744400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr12:118740400-118744400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr12:118740400-118744400	Weak transcription	Osteobl	bone
42	chr12:118740400-118744600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr12:118740400-118748800	Weak transcription	Cortex derived primary cultured neurospheres	brain
44	chr12:118740600-118744200	Weak transcription	HUVEC	blood vessel
45	chr12:118740600-118745000	Weak transcription	Liver	Liver
46	chr12:118740800-118744800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
47	chr12:118740800-118745000	Weak transcription	A549	lung
48	chr12:118740800-118745200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
49	chr12:118741000-118744400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr12:118741000-118744800	Weak transcription	Hela-S3	cervix

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links