Variant report

Variant	rs11169331
Chromosome Location	chr12:50628910-50628911
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	chr12:50628147..50630548-chr12:50634316..50636856,2	MCF-7	breast:

Extended variants
information (count: 129 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:125)

rs_ID	r²[population]
rs10506292	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];0.80[ASN][1000 genomes]
rs10783344	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10783349	0.85[EUR][1000 genomes]
rs10783350	0.83[EUR][1000 genomes]
rs10876013	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10876014	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10876015	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];0.83[YRI][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10876016	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10876017	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10876018	0.83[EUR][1000 genomes]
rs10876023	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[JPT][hapmap]
rs10876024	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[JPT][hapmap]
rs11169314	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11169315	1.00[CEU][hapmap];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11169317	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11169319	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11169322	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11169332	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11169335	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11169339	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11169345	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11169347	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11169348	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];0.86[YRI][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11169349	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11169350	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];0.90[YRI][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11169351	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];0.90[YRI][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11169357	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11169359	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11169360	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11169367	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11169369	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11169370	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11169371	0.84[EUR][1000 genomes]
rs11169373	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11169374	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11169375	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11169376	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11169377	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11169379	0.83[EUR][1000 genomes]
rs11169386	0.82[EUR][1000 genomes]
rs11833608	0.92[CEU][hapmap];1.00[CHB][hapmap];0.83[JPT][hapmap]
rs11836169	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11838347	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12303082	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap]
rs12367872	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap]
rs12422417	1.00[CEU][hapmap];0.94[CHB][hapmap]
rs12424691	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12424713	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12425229	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12425705	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12426444	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12811291	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12821454	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12823506	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12828340	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12832940	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1362983	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17124562	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1972611	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1984993	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2009072	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2111988	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2302900	0.96[CEU][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2358539	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28628775	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34039674	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34614542	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34825838	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34849043	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34858415	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35209607	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35535298	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35663729	0.82[EUR][1000 genomes]
rs35768991	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35878271	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35933908	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3812825	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3861100	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4348979	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap]
rs4421818	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap]
rs4768872	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4768949	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4768951	0.92[CEU][hapmap];0.82[EUR][1000 genomes]
rs6580730	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6580735	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6580736	0.96[CEU][hapmap];0.86[EUR][1000 genomes]
rs6580737	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6580738	0.96[CEU][hapmap];0.86[EUR][1000 genomes]
rs6580739	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6580740	0.84[EUR][1000 genomes]
rs6580741	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs67138019	0.90[EUR][1000 genomes]
rs7132551	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[YRI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7134595	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[JPT][hapmap]
rs7135777	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7138420	0.96[CEU][hapmap]
rs7138622	0.96[CEU][hapmap]
rs71465002	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7295847	0.80[ASN][1000 genomes]
rs7296291	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];0.80[ASN][1000 genomes]
rs7301186	0.80[EUR][1000 genomes]
rs7304445	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7305995	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7308095	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7308885	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7310541	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7311378	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7311491	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7311973	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7312252	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];0.80[ASN][1000 genomes]
rs7314465	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7315690	0.96[CEU][hapmap]
rs7315871	0.83[EUR][1000 genomes]
rs7315955	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7399343	0.83[EUR][1000 genomes]
rs7485486	0.84[EUR][1000 genomes]
rs7486747	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7488682	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7489214	0.83[EUR][1000 genomes]
rs7953953	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7956468	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7974648	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7979830	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7980911	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9705460	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]

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	nsv530671	chr12:50233858-50708991	Flanking Active TSS Active TSS Enhancers Weak transcription Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	117 gene(s)	inside rSNPs	diseases
2	esv3392138	chr12:50394642-50645326	Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
3	nsv899075	chr12:50594947-50835060	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	56 gene(s)	inside rSNPs	diseases
4	esv2761738	chr12:50627292-50836427	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	50 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs11169331	DIP2B	cis	Lymphoblastoid	GTEx
rs11169331	DIP2B	Cis_1M	lymphoblastoid	RTeQTL
rs11169331	CERS5	cis	Nerve Tibial	GTEx
rs11169331	KIAA1463	cis	multi-tissue	Pritchard
rs11169331	DIP2B	cis	multi-tissue	Pritchard

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:50599800-50635800	Weak transcription	Pancreas	Pancrea
2	chr12:50609200-50633200	Weak transcription	Small Intestine	intestine
3	chr12:50616200-50633200	Weak transcription	Lung	lung
4	chr12:50616400-50632000	Weak transcription	Fetal Brain Male	brain
5	chr12:50616400-50634000	Weak transcription	Gastric	stomach
6	chr12:50616400-50634000	Weak transcription	Ovary	ovary
7	chr12:50616400-50636200	Weak transcription	Left Ventricle	heart
8	chr12:50616600-50632200	Weak transcription	Fetal Muscle Trunk	muscle
9	chr12:50616600-50634000	Weak transcription	Colonic Mucosa	Colon
10	chr12:50616600-50634000	Weak transcription	Psoas Muscle	Psoas
11	chr12:50616600-50634000	Weak transcription	Rectal Smooth Muscle	rectum
12	chr12:50616800-50636400	Weak transcription	Aorta	Aorta
13	chr12:50616800-50641600	Weak transcription	Brain Angular Gyrus	brain
14	chr12:50616800-50651800	Weak transcription	Brain Anterior Caudate	brain
15	chr12:50617000-50632800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr12:50617000-50634000	Weak transcription	NHLF	lung
17	chr12:50617000-50636200	Weak transcription	Stomach Smooth Muscle	stomach
18	chr12:50617200-50633000	Strong transcription	Fetal Intestine Small	intestine
19	chr12:50617400-50634600	Weak transcription	Colon Smooth Muscle	Colon
20	chr12:50617400-50635600	Weak transcription	Primary hematopoietic stem cells	blood
21	chr12:50617600-50638400	Weak transcription	Brain Germinal Matrix	brain
22	chr12:50618600-50633800	Weak transcription	NHDF-Ad	bronchial
23	chr12:50618600-50634000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr12:50618600-50634000	Weak transcription	Osteobl	bone
25	chr12:50618600-50634400	Weak transcription	HSMM	muscle
26	chr12:50618600-50636200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
27	chr12:50618600-50638400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr12:50618600-50640000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
29	chr12:50623000-50638400	Weak transcription	Fetal Brain Female	brain
30	chr12:50625400-50634000	Weak transcription	HSMMtube	muscle
31	chr12:50625400-50634400	Weak transcription	Duodenum Smooth Muscle	Duodenum
32	chr12:50626800-50629000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr12:50626800-50633200	Weak transcription	Fetal Muscle Leg	muscle
34	chr12:50627200-50629000	Enhancers	Hela-S3	cervix
35	chr12:50627200-50632800	Weak transcription	Adipose Nuclei	Adipose
36	chr12:50627200-50635200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr12:50627400-50634000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr12:50627600-50634400	Weak transcription	Fetal Lung	lung
39	chr12:50627600-50644600	Weak transcription	Primary T helper cells fromperipheralblood	blood
40	chr12:50628200-50629600	Enhancers	Stomach Mucosa	stomach
41	chr12:50628200-50631400	Strong transcription	Fetal Stomach	stomach
42	chr12:50628400-50634000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr12:50628600-50630400	Weak transcription	Duodenum Mucosa	Duodenum
44	chr12:50628600-50630400	Weak transcription	Skeletal Muscle Female	skeletal muscle
45	chr12:50628600-50632800	Weak transcription	K562	blood
46	chr12:50628600-50634000	Weak transcription	Muscle Satellite Cultured Cells	--
47	chr12:50628600-50634000	Weak transcription	Spleen	Spleen
48	chr12:50628600-50634000	Weak transcription	A549	lung
49	chr12:50628800-50629600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr12:50628800-50630400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links