Variant report

Variant	rs4146922
Chromosome Location	chr2:56067182-56067183
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:55843287..55845090-chr2:56066305..56068048,2	MCF-7	breast:
2	chr2:56066504..56070179-chr2:56070783..56074906,3	MCF-7	breast:
3	chr2:56006332..56008999-chr2:56065171..56067853,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000138041	Chromatin interaction
ENSG00000272606	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10496051	0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10496052	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11125601	0.85[ASN][1000 genomes]
rs11125602	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11125603	0.91[ASN][1000 genomes]
rs11125606	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12464737	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12472893	0.91[ASN][1000 genomes]
rs12615158	0.93[AMR][1000 genomes]
rs1344732	0.80[AMR][1000 genomes]
rs1346782	0.91[ASN][1000 genomes]
rs1346789	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1367225	0.80[AMR][1000 genomes]
rs1430202	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17047234	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17369648	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1946545	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1985162	0.80[AMR][1000 genomes]
rs1985163	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2009262	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3791675	0.90[CEU][hapmap];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs3791679	0.90[CEU][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4146921	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4347871	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs58027672	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs58680090	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs59556444	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs59985551	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62164463	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62167713	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6545522	0.92[ASN][1000 genomes]
rs6724369	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7560657	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7563032	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7591694	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9753383	0.92[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531374	chr2:55653723-56299784	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	56 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Height	25429064	GWAS catalog

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:56064000-56067200	Enhancers	Stomach Mucosa	stomach
2	chr2:56064200-56069400	Enhancers	Breast Myoepithelial Primary Cells	Breast
3	chr2:56064600-56067200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr2:56064800-56067400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr2:56064800-56068800	Weak transcription	Gastric	stomach
6	chr2:56064800-56070200	Weak transcription	K562	blood
7	chr2:56065600-56067400	Enhancers	Fetal Lung	lung
8	chr2:56065800-56067400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr2:56065800-56067400	Enhancers	Muscle Satellite Cultured Cells	--
10	chr2:56065800-56067400	Enhancers	Hela-S3	cervix
11	chr2:56065800-56067400	Enhancers	HSMM	muscle
12	chr2:56065800-56067600	Enhancers	ES-I3 Cell Line	embryonic stem cell
13	chr2:56065800-56067600	Enhancers	HSMMtube	muscle
14	chr2:56066000-56067200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr2:56066000-56067200	Enhancers	Fetal Intestine Small	intestine
16	chr2:56066000-56067200	Flanking Active TSS	HMEC	breast
17	chr2:56066000-56067400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr2:56066000-56067400	Enhancers	HUES64 Cell Line	embryonic stem cell
19	chr2:56066000-56067400	Enhancers	iPS-15b Cell Line	embryonic stem cell
20	chr2:56066000-56067400	Enhancers	Fetal Kidney	kidney
21	chr2:56066000-56067400	Enhancers	Rectal Mucosa Donor 31	rectum
22	chr2:56066000-56067400	Flanking Active TSS	NHEK	skin
23	chr2:56066000-56067600	Enhancers	H9 Cell Line	embryonic stem cell
24	chr2:56066000-56067600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr2:56066200-56067200	Enhancers	Cortex derived primary cultured neurospheres	brain
26	chr2:56066200-56067200	Enhancers	Osteobl	bone
27	chr2:56066200-56067400	Enhancers	Brain Germinal Matrix	brain
28	chr2:56066200-56067600	Enhancers	HUES48 Cell Line	embryonic stem cell
29	chr2:56066400-56067200	Enhancers	Placenta	Placenta
30	chr2:56066600-56067400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr2:56066600-56067600	Flanking Active TSS	A549	lung
32	chr2:56066600-56069600	Weak transcription	Small Intestine	intestine
33	chr2:56066800-56067200	Weak transcription	Pancreas	Pancrea
34	chr2:56066800-56067200	Enhancers	HepG2	liver
35	chr2:56066800-56067400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr2:56066800-56067600	Enhancers	HUES6 Cell Line	embryonic stem cell
37	chr2:56066800-56067800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr2:56066800-56069000	Weak transcription	NHLF	lung
39	chr2:56066800-56069200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr2:56066800-56069600	Weak transcription	Sigmoid Colon	Sigmoid Colon
41	chr2:56066800-56069800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr2:56066800-56070600	Weak transcription	Liver	Liver
43	chr2:56066800-56082600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
44	chr2:56067000-56068200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr2:56067000-56069000	Weak transcription	Fetal Intestine Large	intestine

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