Variant report

Variant	rs2867194
Chromosome Location	chr2:55649449-55649450
allele	C/G
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	EP300	chr2:55649345-55649557	SK-N-SH_RA	brain:	n/a	n/a
2	RCOR1	chr2:55649380-55649456	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:55458950..55461087-chr2:55647562..55649544,2	K562	blood:

Variant related genes	Relation type
CCDC88A	TF binding region
ENSG00000162994	Chromatin interaction
ENSG00000143947	Chromatin interaction

Extended variants
information (count: 117 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:115)

rs_ID	r²[population]
rs10169185	0.89[GIH][hapmap];0.82[JPT][hapmap];0.82[MEX][hapmap]
rs10182704	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10184756	0.82[CEU][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10199332	0.83[YRI][hapmap]
rs10454144	0.88[EUR][1000 genomes]
rs11125565	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11125566	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11125569	0.80[JPT][hapmap]
rs11125572	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11695152	0.83[AFR][1000 genomes]
rs12612806	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12617891	0.92[ASW][hapmap];1.00[CEU][hapmap];0.94[GIH][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12618216	0.87[ASN][1000 genomes]
rs12618795	0.82[CEU][hapmap];0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12623954	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12713297	0.92[ASN][1000 genomes]
rs13394864	0.88[YRI][hapmap]
rs13416912	0.84[EUR][1000 genomes]
rs1454415	0.91[ASN][1000 genomes]
rs1454419	0.93[ASN][1000 genomes]
rs1454420	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1454423	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1454424	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1545554	0.92[ASW][hapmap];1.00[CEU][hapmap];0.94[GIH][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1598163	0.82[GIH][hapmap];0.87[JPT][hapmap]
rs17046959	0.83[YRI][hapmap]
rs1902056	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs1902057	1.00[CEU][hapmap];1.00[GIH][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1902058	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1902061	0.82[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs1902062	0.90[ASN][1000 genomes]
rs2045132	1.00[CEU][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2045133	0.93[EUR][1000 genomes]
rs2045134	0.89[ASN][1000 genomes]
rs2045135	0.91[ASN][1000 genomes]
rs2045136	0.84[ASN][1000 genomes]
rs2123983	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2219130	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2576688	0.85[CEU][hapmap];0.82[GIH][hapmap];0.85[TSI][hapmap];0.90[EUR][1000 genomes]
rs2576703	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs2589057	0.85[CEU][hapmap];0.90[EUR][1000 genomes]
rs2589068	0.85[CEU][hapmap];0.90[EUR][1000 genomes]
rs2589069	0.85[CEU][hapmap];0.90[EUR][1000 genomes]
rs2589070	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs2589078	0.85[CEU][hapmap];0.90[EUR][1000 genomes]
rs2589079	0.90[EUR][1000 genomes]
rs2589104	0.90[EUR][1000 genomes]
rs2864831	1.00[CEU][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2864832	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2867173	0.90[EUR][1000 genomes]
rs2867178	1.00[CEU][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2867179	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2902857	1.00[CEU][hapmap];0.92[YRI][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2903507	0.93[EUR][1000 genomes]
rs2903509	1.00[CEU][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2903514	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2917777	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs2920963	0.86[CEU][hapmap]
rs2920970	1.00[CEU][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2966466	1.00[CEU][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3099080	0.92[ASW][hapmap];1.00[CEU][hapmap];0.85[GIH][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3099081	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs3099083	1.00[CEU][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3111408	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3111409	0.95[EUR][1000 genomes]
rs3748943	0.85[CEU][hapmap];0.92[JPT][hapmap];0.88[YRI][hapmap];0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3762511	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3974263	0.90[EUR][1000 genomes]
rs4233960	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs4233961	1.00[CEU][hapmap];0.94[GIH][hapmap];0.80[JPT][hapmap];0.85[TSI][hapmap];0.93[EUR][1000 genomes]
rs4277563	0.91[ASN][1000 genomes]
rs4481025	1.00[CEU][hapmap];0.82[CHB][hapmap];0.93[JPT][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4535081	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4672032	0.82[CEU][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4672033	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4672035	0.94[GIH][hapmap];0.81[TSI][hapmap]
rs4672036	1.00[CEU][hapmap];0.82[CHB][hapmap];0.93[JPT][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4672037	1.00[CEU][hapmap];0.82[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4672038	1.00[CEU][hapmap];0.82[CHB][hapmap];0.93[JPT][hapmap];0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4672040	0.82[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.93[JPT][hapmap];0.81[TSI][hapmap];0.91[ASN][1000 genomes]
rs4672041	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4672043	1.00[ASN][1000 genomes]
rs4672044	1.00[ASN][1000 genomes]
rs4672045	0.89[GIH][hapmap];0.82[JPT][hapmap];0.82[MEX][hapmap]
rs59634508	0.90[EUR][1000 genomes]
rs61157332	0.90[EUR][1000 genomes]
rs6545489	0.95[YRI][hapmap];0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6545490	1.00[CEU][hapmap];0.97[GIH][hapmap];0.80[JPT][hapmap];0.85[TSI][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6545491	1.00[CEU][hapmap];0.82[CHB][hapmap];0.93[JPT][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6545492	0.90[JPT][hapmap];0.91[ASN][1000 genomes]
rs6709204	1.00[CEU][hapmap];1.00[GIH][hapmap];0.93[TSI][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6710192	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs6718031	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6718909	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6720698	0.82[CHB][hapmap];0.93[JPT][hapmap];0.92[ASN][1000 genomes]
rs6721593	0.82[CEU][hapmap];0.91[JPT][hapmap];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6724840	0.82[CEU][hapmap];0.95[YRI][hapmap];0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6725968	1.00[CEU][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6729490	0.81[AFR][1000 genomes]
rs6732633	0.80[AFR][1000 genomes];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6732759	0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6733814	0.91[ASN][1000 genomes]
rs6744426	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6748979	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72924907	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7424286	0.87[ASN][1000 genomes]
rs7557555	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7557956	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7559987	0.80[JPT][hapmap]
rs7579037	0.82[CHB][hapmap];0.93[JPT][hapmap];0.91[ASN][1000 genomes]
rs7586440	1.00[CEU][hapmap];0.91[YRI][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7601340	0.81[JPT][hapmap]
rs7601588	0.92[ASW][hapmap];1.00[CEU][hapmap];0.94[GIH][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7602189	0.91[ASN][1000 genomes]
rs7606361	0.92[ASW][hapmap];1.00[CEU][hapmap];0.85[GIH][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]

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	nsv1006170	chr2:55530179-55809251	Strong transcription Weak transcription Bivalent/Poised TSS Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv520581	chr2:55622825-55903016	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2867194	FLJ31438	cis	multi-tissue	Pritchard

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55647800-55652400	Weak transcription	Stomach Mucosa	stomach
2	chr2:55648000-55649800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr2:55648000-55649800	Weak transcription	Colon Smooth Muscle	Colon
4	chr2:55648000-55650000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr2:55648000-55650000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr2:55648000-55650000	Enhancers	Primary hematopoietic stem cells short term culture	blood
7	chr2:55648000-55650000	Enhancers	Brain Germinal Matrix	brain
8	chr2:55648000-55651000	Weak transcription	HMEC	breast
9	chr2:55648000-55651200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
10	chr2:55648000-55651600	Weak transcription	NHEK	skin
11	chr2:55648000-55652200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr2:55648000-55652200	Weak transcription	HUVEC	blood vessel
13	chr2:55648000-55652200	Weak transcription	NH-A	brain
14	chr2:55648000-55652400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr2:55648000-55652400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr2:55648000-55652400	Weak transcription	HSMM	muscle
17	chr2:55648000-55653400	Enhancers	Primary monocytes fromperipheralblood	blood
18	chr2:55648000-55659000	Weak transcription	Adipose Nuclei	Adipose
19	chr2:55648200-55650000	Enhancers	Primary hematopoietic stem cells	blood
20	chr2:55648200-55651000	Weak transcription	Muscle Satellite Cultured Cells	--
21	chr2:55648200-55651200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr2:55648200-55652200	Weak transcription	Osteobl	bone
23	chr2:55648400-55649600	Weak transcription	Brain Substantia Nigra	brain
24	chr2:55648400-55650000	Weak transcription	Brain Anterior Caudate	brain
25	chr2:55648400-55650200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr2:55648400-55651800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr2:55648400-55652400	Weak transcription	Primary neutrophils fromperipheralblood	blood
28	chr2:55648400-55652400	Enhancers	A549	lung
29	chr2:55648400-55652400	Enhancers	Monocytes-CD14+_RO01746	blood
30	chr2:55648600-55649600	Weak transcription	Brain Hippocampus Middle	brain
31	chr2:55648600-55650000	Weak transcription	Brain Angular Gyrus	brain
32	chr2:55648600-55650400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr2:55648600-55651000	Weak transcription	Brain Cingulate Gyrus	brain
34	chr2:55648600-55651200	Weak transcription	K562	blood
35	chr2:55648800-55650000	Weak transcription	GM12878-XiMat	blood
36	chr2:55648800-55650200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr2:55649000-55650000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr2:55649200-55649600	Enhancers	Fetal Heart	heart
39	chr2:55649200-55649600	Enhancers	Fetal Lung	lung
40	chr2:55649200-55649600	Weak transcription	HepG2	liver
41	chr2:55649200-55651000	Weak transcription	NHLF	lung
42	chr2:55649400-55649600	Enhancers	Dnd41	blood
43	chr2:55649400-55650000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr2:55649400-55650200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr2:55649400-55651400	Weak transcription	NHDF-Ad	bronchial
46	chr2:55649400-55652200	Enhancers	Hela-S3	cervix

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links