Variant report

Variant	rs4832300
Chromosome Location	chr2:86788513-86788514
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	chr2:86788281-86788664	MCF10A-Er-Src	breast:	n/a	n/a
2	POLR2A	chr2:86788139-86791058	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:86788265..86792368-chr2:86847223..86851122,9	MCF-7	breast:
2	chr2:86787885..86791617-chr2:86846945..86852237,10	MCF-7	breast:
3	chr2:86683337..86686158-chr2:86788468..86790099,2	K562	blood:

Variant related genes	Relation type
ENSG00000228363	TF binding region
ENSG00000115548	Chromatin interaction
ENSG00000249884	Chromatin interaction
ENSG00000239305	Chromatin interaction

Extended variants
information (count: 86 )
Associated
traits (count: 5 )

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

rs_ID	r²[population]
rs1015117	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10169746	0.98[ASN][1000 genomes]
rs10180036	0.93[CEU][hapmap];0.85[YRI][hapmap]
rs10184879	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10184985	0.81[ASN][1000 genomes]
rs10187753	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10187880	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10188515	0.91[ASN][1000 genomes]
rs1020306	0.83[EUR][1000 genomes]
rs10432704	1.00[ASN][1000 genomes]
rs1080551	0.98[ASN][1000 genomes]
rs11127045	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11127046	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11127047	0.81[CHD][hapmap];0.81[GIH][hapmap]
rs1137684	0.80[AFR][1000 genomes];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11676576	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11684230	0.80[AFR][1000 genomes];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11689330	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11689593	0.97[ASN][1000 genomes]
rs12328637	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12613282	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12614447	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12615285	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12623509	0.96[CEU][hapmap];1.00[CHB][hapmap];0.89[GIH][hapmap];0.88[MEX][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12714186	0.96[CEU][hapmap];0.83[GIH][hapmap];0.80[LWK][hapmap];0.93[TSI][hapmap]
rs12714188	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12714190	1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.94[ASN][1000 genomes]
rs12714198	0.86[ASW][hapmap];0.96[CEU][hapmap];0.90[CHD][hapmap];0.85[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap]
rs12714199	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs12987172	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][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]
rs12991654	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13015620	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13034615	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13390713	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13408041	0.80[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13429696	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1465813	0.80[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs1518807	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1629293	1.00[CHB][hapmap];0.94[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.90[MKK][hapmap];0.82[TSI][hapmap];0.93[ASN][1000 genomes]
rs218059	0.91[ASN][1000 genomes]
rs2241803	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs2292887	1.00[ASW][hapmap];0.96[CEU][hapmap];0.81[GIH][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs308900	0.81[ASN][1000 genomes]
rs308902	0.91[GIH][hapmap]
rs308903	0.89[GIH][hapmap]
rs308910	0.93[GIH][hapmap];0.82[TSI][hapmap]
rs308914	0.95[GIH][hapmap];0.87[MKK][hapmap];0.80[TSI][hapmap]
rs308915	0.87[GIH][hapmap]
rs3201448	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs34666164	0.98[ASN][1000 genomes]
rs3731812	0.80[AFR][1000 genomes];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3755002	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes]
rs3770058	0.80[AFR][1000 genomes]
rs422240	0.94[CHD][hapmap];0.93[GIH][hapmap];0.85[JPT][hapmap];0.88[MKK][hapmap];0.82[TSI][hapmap]
rs4832040	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4832041	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4832042	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4832043	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4832045	0.95[ASN][1000 genomes]
rs4832296	0.94[ASN][1000 genomes]
rs4832297	1.00[CEU][hapmap];0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4832299	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4832302	0.98[ASN][1000 genomes]
rs4832303	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4832304	1.00[ASW][hapmap];1.00[CEU][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];0.85[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62147239	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6725080	0.80[AFR][1000 genomes]
rs6728211	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6731025	0.88[ASN][1000 genomes]
rs6733569	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6738663	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[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];0.99[ASN][1000 genomes]
rs6750226	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.93[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]
rs6752371	1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];1.00[ASN][1000 genomes]
rs7369138	0.80[AFR][1000 genomes];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7557796	0.88[CHB][hapmap];0.81[GIH][hapmap]
rs7568840	0.88[CHB][hapmap];0.81[ASN][1000 genomes]
rs7570640	0.98[ASN][1000 genomes]
rs7584882	1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.94[JPT][hapmap];1.00[ASN][1000 genomes]
rs7593151	0.94[ASN][1000 genomes]
rs7596717	1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.94[ASN][1000 genomes]
rs7601115	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8179729	0.94[ASN][1000 genomes]
rs9284788	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs958561	0.86[ASW][hapmap];0.96[CEU][hapmap];0.91[LWK][hapmap];0.98[MKK][hapmap];0.93[TSI][hapmap];0.85[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3412938	chr2:86370969-86867936	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	77 gene(s)	inside rSNPs	diseases
2	nsv532724	chr2:86622295-87086407	Weak transcription Active TSS Genic enhancers Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs4832300	POLR1A	cis	parietal	SCAN
rs4832300	C2orf68	cis	cerebellum	SCAN
rs4832300	VPS24	Cis_1M	lymphoblastoid	RTeQTL
rs4832300	POLR1A	cis	cerebellum	SCAN
rs4832300	VPS24	cis	lymphoblastoid	seeQTL

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:86756600-86789200	Weak transcription	Aorta	Aorta
2	chr2:86761200-86788600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr2:86761200-86788800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr2:86774400-86788800	Weak transcription	Fetal Lung	lung
5	chr2:86775200-86788800	Weak transcription	Duodenum Mucosa	Duodenum
6	chr2:86776800-86788800	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr2:86777400-86789200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr2:86777400-86789600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr2:86777600-86789200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr2:86777600-86789400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr2:86777600-86789400	Weak transcription	Lung	lung
12	chr2:86777800-86789400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr2:86778200-86789000	Weak transcription	NHLF	lung
14	chr2:86779400-86788800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr2:86779400-86789400	Weak transcription	Placenta	Placenta
16	chr2:86780200-86789000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr2:86780600-86788600	Enhancers	Primary T helper cells fromperipheralblood	blood
18	chr2:86780800-86789400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
19	chr2:86780800-86789600	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr2:86781200-86788800	Weak transcription	Cortex derived primary cultured neurospheres	brain
21	chr2:86782600-86789000	Enhancers	Primary T helper cells PMA-I stimulated	--
22	chr2:86782800-86788600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr2:86783000-86789200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
24	chr2:86783200-86789400	Weak transcription	Fetal Thymus	thymus
25	chr2:86784400-86789400	Weak transcription	Primary T cells fromperipheralblood	blood
26	chr2:86784400-86789400	Weak transcription	Fetal Muscle Leg	muscle
27	chr2:86784600-86789200	Enhancers	Primary T helper naive cells from peripheral blood	blood
28	chr2:86784600-86789200	Weak transcription	Psoas Muscle	Psoas
29	chr2:86784800-86789000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr2:86784800-86789400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr2:86784800-86789400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
32	chr2:86785000-86789200	Weak transcription	Fetal Intestine Large	intestine
33	chr2:86785400-86789200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr2:86785800-86788600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
35	chr2:86785800-86788800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr2:86785800-86788800	Weak transcription	Stomach Smooth Muscle	stomach
37	chr2:86786000-86788800	Weak transcription	Brain Substantia Nigra	brain
38	chr2:86786000-86789000	Weak transcription	Osteobl	bone
39	chr2:86786400-86789400	Weak transcription	Pancreas	Pancrea
40	chr2:86786400-86789600	Weak transcription	Gastric	stomach
41	chr2:86787000-86788800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr2:86787000-86788800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
43	chr2:86787000-86789200	Weak transcription	HSMMtube	muscle
44	chr2:86787000-86789400	Weak transcription	Fetal Muscle Trunk	muscle
45	chr2:86787200-86788600	Weak transcription	A549	lung
46	chr2:86787200-86789200	Weak transcription	Fetal Brain Male	brain
47	chr2:86787400-86789000	Weak transcription	Fetal Stomach	stomach
48	chr2:86787600-86789400	Weak transcription	H1 Cell Line	embryonic stem cell
49	chr2:86787800-86788600	Enhancers	Ovary	ovary
50	chr2:86787800-86788800	Genic enhancers	Left Ventricle	heart

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links