Variant report

Variant	rs2896489
Chromosome Location	chr14:104108743-104108744
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 82 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs10047805	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10131067	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1054080	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1078756	0.82[ASN][1000 genomes]
rs11160754	0.84[ASN][1000 genomes]
rs11160756	1.00[CEU][hapmap];0.80[CHB][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11625397	0.87[JPT][hapmap];0.87[MEX][hapmap]
rs11626589	0.83[ASN][1000 genomes]
rs11848721	0.81[ASN][1000 genomes]
rs11850979	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];0.96[YRI][hapmap];0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12434218	0.81[JPT][hapmap]
rs12435399	0.82[ASN][1000 genomes]
rs12881418	0.83[JPT][hapmap]
rs12897511	0.84[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs2296483	0.87[JPT][hapmap];0.91[MEX][hapmap]
rs2403202	0.82[CEU][hapmap]
rs2403203	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28798508	0.82[ASN][1000 genomes]
rs28823639	0.82[ASN][1000 genomes]
rs2896488	0.80[ASN][1000 genomes]
rs3212136	0.83[JPT][hapmap]
rs35015260	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35686878	0.86[ASN][1000 genomes]
rs3742463	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3742465	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[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3759586	0.86[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4318144	0.81[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs4374097	0.82[ASN][1000 genomes]
rs4383078	0.82[ASN][1000 genomes]
rs4444269	0.82[ASN][1000 genomes]
rs4561394	0.92[ASN][1000 genomes]
rs4900583	0.88[ASN][1000 genomes]
rs4900584	0.88[ASN][1000 genomes]
rs4900586	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4900587	0.83[JPT][hapmap]
rs4900589	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4906340	0.83[ASN][1000 genomes]
rs4906341	0.81[ASN][1000 genomes]
rs4906342	0.84[ASN][1000 genomes]
rs4906348	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4906349	0.88[ASN][1000 genomes]
rs4906352	0.83[ASN][1000 genomes]
rs4906355	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4906358	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs58601596	0.81[ASN][1000 genomes]
rs61436277	0.89[ASN][1000 genomes]
rs61995761	0.81[ASN][1000 genomes]
rs709399	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7145234	0.82[ASN][1000 genomes]
rs7154572	1.00[CHB][hapmap];0.93[CHD][hapmap];0.91[JPT][hapmap];0.92[ASN][1000 genomes]
rs7155511	0.89[ASN][1000 genomes]
rs7156832	0.91[ASN][1000 genomes]
rs7157116	0.81[ASN][1000 genomes]
rs7161125	0.82[ASN][1000 genomes]
rs729437	0.91[CEU][hapmap];0.86[CHB][hapmap];0.82[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.92[TSI][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs745079	0.91[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.87[TSI][hapmap];0.89[YRI][hapmap];0.82[ASN][1000 genomes]
rs752624	0.87[JPT][hapmap];0.87[MEX][hapmap]
rs8003289	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8007489	0.89[CHD][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.96[MEX][hapmap];0.82[ASN][1000 genomes]
rs8007903	1.00[CHB][hapmap];0.91[CHD][hapmap];0.91[JPT][hapmap]
rs8007915	1.00[CEU][hapmap];0.86[CHB][hapmap];0.89[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8008451	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];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8018214	0.91[ASN][1000 genomes]
rs8021368	0.91[GIH][hapmap];0.95[JPT][hapmap];0.89[TSI][hapmap];0.81[ASN][1000 genomes]
rs8021904	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs861530	0.95[CEU][hapmap];0.81[CHB][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs861537	0.91[CEU][hapmap];0.82[CHB][hapmap];0.98[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs861544	0.94[ASW][hapmap];0.95[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.96[MEX][hapmap];0.91[TSI][hapmap];0.96[YRI][hapmap];0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs861545	1.00[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs861547	1.00[CEU][hapmap];0.86[CHB][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs8702	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3332028	chr14:103581471-104328811	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	162 gene(s)	inside rSNPs	diseases
2	nsv832883	chr14:103927687-104120953	Genic enhancers Weak transcription Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
3	nsv902300	chr14:103967504-104205811	Active TSS Enhancers Bivalent Enhancer Flanking Active TSS Genic enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
4	nsv1052010	chr14:104061472-104216267	Weak transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
5	nsv542201	chr14:104061472-104216267	Weak transcription Enhancers Genic enhancers Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
6	nsv456435	chr14:104061646-104198251	Weak transcription Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	52 gene(s)	inside rSNPs	diseases
7	nsv566023	chr14:104061646-104198251	Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	52 gene(s)	inside rSNPs	diseases
8	nsv902308	chr14:104087209-104211180	Enhancers Genic enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
9	nsv1041329	chr14:104097750-104196346	Strong transcription Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
10	nsv542202	chr14:104097750-104196346	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
11	nsv1048866	chr14:104100862-104195896	Weak transcription Active TSS Flanking Active TSS Genic enhancers Strong transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs2896489	ZFYVE21	cis	Lymphoblastoid	GTEx
rs2896489	KLC1	cis	parietal	SCAN
rs2896489	ZFYVE21	cis	lymphoblastoid	seeQTL
rs2896489	CAMK2G	trans	parietal	SCAN
rs2896489	ZFYVE21	cis	multi-tissue	Pritchard
rs2896489	XRCC3	cis	lymphoblastoid	seeQTL

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:104096600-104118000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr14:104097400-104117800	Weak transcription	Primary monocytes fromperipheralblood	blood
3	chr14:104097400-104119400	Weak transcription	HSMMtube	muscle
4	chr14:104097400-104120000	Weak transcription	HUES64 Cell Line	embryonic stem cell
5	chr14:104097400-104120000	Weak transcription	HUVEC	blood vessel
6	chr14:104097400-104120200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr14:104097400-104120200	Weak transcription	Colonic Mucosa	Colon
8	chr14:104097400-104120200	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr14:104097400-104120400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
10	chr14:104097400-104120400	Weak transcription	Rectal Mucosa Donor 29	rectum
11	chr14:104097400-104120800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr14:104097400-104156600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr14:104098600-104119200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr14:104098600-104119800	Weak transcription	K562	blood
15	chr14:104099200-104120200	Weak transcription	HUES48 Cell Line	embryonic stem cell
16	chr14:104100000-104119400	Weak transcription	Placenta	Placenta
17	chr14:104101000-104120200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr14:104101200-104120600	Weak transcription	Brain Germinal Matrix	brain
19	chr14:104101600-104119400	Weak transcription	Primary neutrophils fromperipheralblood	blood
20	chr14:104101800-104120800	Weak transcription	Hela-S3	cervix
21	chr14:104102600-104111600	Weak transcription	Primary T cells from cord blood	blood
22	chr14:104102600-104120000	Weak transcription	Primary hematopoietic stem cells	blood
23	chr14:104102800-104118400	Weak transcription	Primary B cells from cord blood	blood
24	chr14:104103000-104119200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr14:104103000-104119400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr14:104104400-104118000	Weak transcription	A549	lung
27	chr14:104104400-104119400	Weak transcription	Fetal Thymus	thymus
28	chr14:104104600-104112400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
29	chr14:104104600-104114600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
30	chr14:104104600-104114800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr14:104104600-104115000	Weak transcription	Fetal Muscle Leg	muscle
32	chr14:104104600-104118000	Weak transcription	Brain Hippocampus Middle	brain
33	chr14:104104600-104119600	Weak transcription	Thymus	Thymus
34	chr14:104104600-104120200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr14:104104800-104120200	Weak transcription	Fetal Intestine Large	intestine
36	chr14:104104800-104120400	Weak transcription	Liver	Liver
37	chr14:104104800-104120800	Weak transcription	HepG2	liver
38	chr14:104105000-104112400	Weak transcription	Cortex derived primary cultured neurospheres	brain
39	chr14:104105000-104117800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr14:104105200-104117800	Weak transcription	Aorta	Aorta
41	chr14:104105200-104117800	Weak transcription	Brain Substantia Nigra	brain
42	chr14:104105200-104118000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr14:104105200-104120200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
44	chr14:104105200-104121800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
45	chr14:104105200-104122200	Weak transcription	Fetal Kidney	kidney
46	chr14:104105400-104109000	Weak transcription	Ovary	ovary
47	chr14:104105400-104111600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr14:104105400-104111600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
49	chr14:104105400-104111600	Weak transcription	Lung	lung
50	chr14:104105400-104111800	Weak transcription	Gastric	stomach

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links