Variant report

Variant	rs2302900
Chromosome Location	chr12:50599709-50599710
allele	C/T
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	POLR2A	chr12:50598607-50599741	U87	brain:	n/a	n/a
2	POLR2A	chr12:50599137-50599711	U87	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:50597958..50602856-chr12:50604694..50610518,6	K562	blood:
2	chr12:50596667..50602931-chr12:50613575..50616735,6	K562	blood:
3	chr12:50598358..50601280-chr12:50607490..50609263,3	K562	blood:

Variant related genes	Relation type
LIMA1	TF binding region
ENSG00000050405	Chromatin interaction

Extended variants
information (count: 115 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:112)

rs_ID	r²[population]
rs10506292	0.96[CEU][hapmap]
rs10783344	0.96[CEU][hapmap];0.88[YRI][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10876013	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10876014	0.96[CEU][hapmap];0.87[GIH][hapmap];0.84[MEX][hapmap];0.93[TSI][hapmap];0.88[YRI][hapmap];0.87[EUR][1000 genomes]
rs10876015	0.96[CEU][hapmap];0.84[MEX][hapmap];0.93[TSI][hapmap];0.86[EUR][1000 genomes]
rs10876016	0.86[EUR][1000 genomes]
rs10876017	0.96[CEU][hapmap];0.87[GIH][hapmap];0.84[MEX][hapmap];0.93[TSI][hapmap];0.88[YRI][hapmap];0.86[EUR][1000 genomes]
rs10876023	0.96[CEU][hapmap]
rs10876024	0.95[CEU][hapmap]
rs11169314	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11169315	0.96[CEU][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11169317	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11169319	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11169322	1.00[CEU][hapmap];0.91[GIH][hapmap];0.91[TSI][hapmap];0.88[YRI][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11169331	0.96[CEU][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11169332	0.96[CEU][hapmap];0.84[MEX][hapmap];0.93[TSI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11169335	0.96[CEU][hapmap];0.84[MEX][hapmap];0.93[TSI][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11169339	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11169345	0.87[EUR][1000 genomes]
rs11169347	0.87[EUR][1000 genomes]
rs11169348	0.96[CEU][hapmap];0.83[MEX][hapmap];0.89[TSI][hapmap];0.86[EUR][1000 genomes]
rs11169349	0.86[EUR][1000 genomes]
rs11169350	0.96[CEU][hapmap];0.86[EUR][1000 genomes]
rs11169351	0.96[CEU][hapmap];0.84[MEX][hapmap];0.93[TSI][hapmap];0.86[EUR][1000 genomes]
rs11169357	0.96[CEU][hapmap];0.87[YRI][hapmap];0.86[EUR][1000 genomes]
rs11169359	0.85[EUR][1000 genomes]
rs11169360	0.95[CEU][hapmap];0.88[YRI][hapmap];0.87[EUR][1000 genomes]
rs11169367	0.82[EUR][1000 genomes]
rs11169369	0.85[EUR][1000 genomes]
rs11169370	0.96[CEU][hapmap];0.87[GIH][hapmap];0.84[MEX][hapmap];0.93[TSI][hapmap];0.88[YRI][hapmap];0.86[EUR][1000 genomes]
rs11169373	0.85[EUR][1000 genomes]
rs11169374	0.85[EUR][1000 genomes]
rs11169375	0.82[EUR][1000 genomes]
rs11169376	0.82[EUR][1000 genomes]
rs11169377	0.82[EUR][1000 genomes]
rs11833608	0.88[CEU][hapmap];0.87[GIH][hapmap];0.84[MEX][hapmap];0.93[TSI][hapmap];0.88[YRI][hapmap]
rs11836169	0.82[EUR][1000 genomes]
rs11838347	0.96[CEU][hapmap];0.87[GIH][hapmap];0.83[MEX][hapmap];0.93[TSI][hapmap];0.88[YRI][hapmap];0.87[EUR][1000 genomes]
rs12303082	0.96[CEU][hapmap];0.84[MEX][hapmap];0.93[TSI][hapmap]
rs12367872	0.96[CEU][hapmap];0.89[GIH][hapmap];0.83[MEX][hapmap];0.91[TSI][hapmap]
rs12422417	0.96[CEU][hapmap];0.84[MEX][hapmap];0.93[TSI][hapmap]
rs12424691	0.96[CEU][hapmap];0.89[GIH][hapmap];0.84[MEX][hapmap];0.93[TSI][hapmap];0.88[YRI][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12424713	0.96[CEU][hapmap];0.88[YRI][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12425229	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12425705	0.96[CEU][hapmap];0.89[GIH][hapmap];0.82[MEX][hapmap];0.93[TSI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12811291	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12821454	0.87[EUR][1000 genomes]
rs12823506	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12828340	0.96[CEU][hapmap];0.87[GIH][hapmap];0.84[MEX][hapmap];0.93[TSI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12832940	0.87[EUR][1000 genomes]
rs1362983	0.96[CEU][hapmap];0.89[GIH][hapmap];0.83[MEX][hapmap];0.93[TSI][hapmap];0.83[YRI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17124562	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1972611	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2009072	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2111988	0.96[CEU][hapmap];0.87[GIH][hapmap];0.84[MEX][hapmap];0.93[TSI][hapmap];0.88[YRI][hapmap];0.87[EUR][1000 genomes]
rs2358539	0.96[CEU][hapmap];0.84[MEX][hapmap];0.93[TSI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs28628775	0.86[EUR][1000 genomes]
rs3184122	0.82[MKK][hapmap]
rs34039674	0.81[EUR][1000 genomes]
rs34614542	0.82[EUR][1000 genomes]
rs34825838	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs34849043	0.83[EUR][1000 genomes]
rs34858415	0.82[EUR][1000 genomes]
rs35209607	0.85[EUR][1000 genomes]
rs35535298	0.87[EUR][1000 genomes]
rs35663729	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35768991	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs35878271	0.81[EUR][1000 genomes]
rs35933908	0.86[EUR][1000 genomes]
rs3812825	0.96[CEU][hapmap];0.89[GIH][hapmap];0.93[TSI][hapmap];0.87[YRI][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3861100	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4348979	0.96[CEU][hapmap];0.93[TSI][hapmap]
rs4421818	0.96[CEU][hapmap];0.87[GIH][hapmap];0.84[MEX][hapmap];0.93[TSI][hapmap];0.88[YRI][hapmap]
rs4768872	0.81[EUR][1000 genomes]
rs4768949	0.80[EUR][1000 genomes]
rs4768951	0.92[CEU][hapmap]
rs6580730	0.81[AMR][1000 genomes]
rs6580735	0.87[EUR][1000 genomes]
rs6580736	0.92[CEU][hapmap];0.85[TSI][hapmap];0.81[EUR][1000 genomes]
rs6580737	0.86[EUR][1000 genomes]
rs6580738	0.92[CEU][hapmap];0.85[TSI][hapmap];0.81[EUR][1000 genomes]
rs6580739	0.81[EUR][1000 genomes]
rs6580741	0.81[EUR][1000 genomes]
rs67138019	0.87[EUR][1000 genomes]
rs7132551	0.96[CEU][hapmap];0.83[MEX][hapmap];0.93[TSI][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7134595	0.96[CEU][hapmap];0.87[GIH][hapmap];0.84[MEX][hapmap];0.93[TSI][hapmap];0.88[YRI][hapmap]
rs7135777	0.87[EUR][1000 genomes]
rs7138420	0.91[CEU][hapmap]
rs7138622	0.91[CEU][hapmap]
rs71465002	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7296291	0.96[CEU][hapmap];0.82[MEX][hapmap];0.93[TSI][hapmap]
rs7304445	0.86[EUR][1000 genomes]
rs7305995	0.87[EUR][1000 genomes]
rs7308095	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7308885	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7310541	0.82[EUR][1000 genomes]
rs7311378	0.87[EUR][1000 genomes]
rs7311491	0.87[EUR][1000 genomes]
rs7311973	0.95[CEU][hapmap];0.86[EUR][1000 genomes]
rs7312252	0.96[CEU][hapmap];0.84[MEX][hapmap];0.93[TSI][hapmap]
rs7314465	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7315690	0.91[CEU][hapmap]
rs7315871	0.84[EUR][1000 genomes]
rs7315955	0.80[EUR][1000 genomes]
rs7486747	0.96[CEU][hapmap];0.91[TSI][hapmap];0.91[YRI][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7488682	0.86[EUR][1000 genomes]
rs7953953	0.96[CEU][hapmap];0.87[GIH][hapmap];0.84[MEX][hapmap];0.93[TSI][hapmap];0.88[YRI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7956468	0.86[EUR][1000 genomes]
rs7974648	0.81[EUR][1000 genomes]
rs7979830	0.96[CEU][hapmap];0.87[YRI][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7980911	0.87[EUR][1000 genomes]
rs9705460	0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs2302900	CERS5	cis	Nerve Tibial	GTEx
rs2302900	LASS5	cis	cerebellum	SCAN
rs2302900	LASS5	cis	parietal	SCAN
rs2302900	FAIM2	cis	cerebellum	SCAN
rs2302900	CELA1	cis	parietal	SCAN
rs2302900	DIP2B	cis	multi-tissue	Pritchard
rs2302900	KIAA1463	cis	multi-tissue	Pritchard
rs2302900	SLC38A1	cis	parietal	SCAN
rs2302900	ATF1	cis	Artery Tibial	GTEx
rs2302900	DIP2B	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:50564400-50600800	Weak transcription	Primary monocytes fromperipheralblood	blood
2	chr12:50570000-50601400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr12:50571800-50614200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr12:50572200-50614000	Weak transcription	Right Ventricle	heart
5	chr12:50581800-50601000	Weak transcription	Brain Substantia Nigra	brain
6	chr12:50582400-50600000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr12:50582800-50614000	Weak transcription	Brain Angular Gyrus	brain
8	chr12:50582800-50614200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr12:50583000-50614400	Weak transcription	Brain Anterior Caudate	brain
10	chr12:50583400-50600800	Strong transcription	Adipose Nuclei	Adipose
11	chr12:50585200-50604000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
12	chr12:50585200-50604000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
13	chr12:50587800-50599800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
14	chr12:50588000-50599800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr12:50588400-50600200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr12:50588400-50600600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr12:50588400-50600600	Strong transcription	Primary T cells fromperipheralblood	blood
18	chr12:50589400-50599800	Strong transcription	Primary T helper cells PMA-I stimulated	--
19	chr12:50589400-50599800	Strong transcription	GM12878-XiMat	blood
20	chr12:50589400-50600800	Strong transcription	Cortex derived primary cultured neurospheres	brain
21	chr12:50590600-50600000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr12:50590600-50600200	Strong transcription	Fetal Thymus	thymus
23	chr12:50590800-50599800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
24	chr12:50590800-50600000	Weak transcription	Pancreatic Islets	Pancreatic Islet
25	chr12:50591000-50600200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr12:50591000-50603000	Strong transcription	Fetal Muscle Trunk	muscle
27	chr12:50591600-50600000	Strong transcription	Duodenum Smooth Muscle	Duodenum
28	chr12:50591600-50615600	Weak transcription	HepG2	liver
29	chr12:50592000-50600200	Strong transcription	Stomach Smooth Muscle	stomach
30	chr12:50593400-50614200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr12:50593400-50614200	Weak transcription	Fetal Brain Male	brain
32	chr12:50593400-50614600	Weak transcription	Esophagus	oesophagus
33	chr12:50594000-50599800	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
34	chr12:50594400-50599800	Strong transcription	Rectal Smooth Muscle	rectum
35	chr12:50595600-50599800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
36	chr12:50595600-50600600	Strong transcription	Primary T cells from cord blood	blood
37	chr12:50595800-50600800	Strong transcription	Fetal Muscle Leg	muscle
38	chr12:50596200-50613400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
39	chr12:50596400-50600600	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr12:50596400-50600800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr12:50596600-50600600	Strong transcription	HSMMtube	muscle
42	chr12:50596600-50604600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr12:50596600-50605400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr12:50596600-50607200	Strong transcription	Fetal Intestine Small	intestine
45	chr12:50596800-50599800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
46	chr12:50596800-50599800	Strong transcription	Dnd41	blood
47	chr12:50596800-50600000	Strong transcription	HUES64 Cell Line	embryonic stem cell
48	chr12:50596800-50600800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr12:50596800-50601400	Strong transcription	HSMM	muscle
50	chr12:50596800-50604200	Strong transcription	Fetal Stomach	stomach

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