Variant report

Variant	rs1896883
Chromosome Location	chr4:152595373-152595374
allele	A/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	POLR2A	chr4:152595145-152595546	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr4:152595140-152595407	H1-hESC	embryonic stem cell:	n/a	n/a
3	GATA1	chr4:152594694-152595511	PBDE	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:152586811..152588784-chr4:152594944..152597793,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000251455	TF binding region
ENSG00000251603	Chromatin interaction

Extended variants
information (count: 103 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:100)

rs_ID	r²[population]
rs10007015	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10007167	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10019048	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.95[TSI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10023298	0.86[EUR][1000 genomes]
rs10028410	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10028961	0.86[EUR][1000 genomes]
rs10049728	0.95[CEU][hapmap];0.86[EUR][1000 genomes]
rs10049991	0.86[EUR][1000 genomes]
rs10776524	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1105534	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1105535	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1105536	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11734799	0.81[EUR][1000 genomes]
rs12331037	1.00[CEU][hapmap];0.82[CHB][hapmap];0.82[GIH][hapmap];0.87[MEX][hapmap];0.86[TSI][hapmap];0.85[EUR][1000 genomes]
rs12502055	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12641433	0.82[GIH][hapmap]
rs13137669	0.82[EUR][1000 genomes]
rs13138986	0.81[EUR][1000 genomes]
rs13146981	0.81[EUR][1000 genomes]
rs13149588	0.92[CEU][hapmap]
rs1355413	1.00[CEU][hapmap];0.86[CHB][hapmap];0.90[EUR][1000 genomes]
rs1366909	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1511170	0.84[EUR][1000 genomes]
rs17027798	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17360475	1.00[CEU][hapmap];0.82[CHB][hapmap];0.82[GIH][hapmap];0.86[TSI][hapmap];0.86[EUR][1000 genomes]
rs1864300	0.85[EUR][1000 genomes]
rs1877187	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2007218	1.00[CEU][hapmap];0.82[CHB][hapmap];0.84[GIH][hapmap];0.83[MEX][hapmap];0.86[TSI][hapmap];0.88[EUR][1000 genomes]
rs2007445	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2278304	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap]
rs2303866	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs2406973	0.82[GIH][hapmap]
rs2840130	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28637056	0.87[EUR][1000 genomes]
rs28710456	0.86[EUR][1000 genomes]
rs3749561	1.00[CEU][hapmap];0.86[CHB][hapmap];0.91[CHD][hapmap];0.87[GIH][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3749563	1.00[CEU][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3792691	1.00[CEU][hapmap];0.86[CHB][hapmap];0.88[CHD][hapmap];0.84[GIH][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap];0.91[EUR][1000 genomes]
rs3919716	0.84[EUR][1000 genomes]
rs4383600	0.84[EUR][1000 genomes]
rs4571	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4696104	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4696109	1.00[CEU][hapmap];0.82[CHB][hapmap];0.82[GIH][hapmap];0.87[MEX][hapmap];0.86[TSI][hapmap];0.86[EUR][1000 genomes]
rs4696111	0.86[EUR][1000 genomes]
rs4696277	0.93[EUR][1000 genomes]
rs4696283	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4696284	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4696285	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.89[MKK][hapmap];0.93[TSI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4696291	0.90[EUR][1000 genomes]
rs4696293	0.96[CEU][hapmap];0.82[GIH][hapmap];0.87[MEX][hapmap];0.84[TSI][hapmap];0.83[EUR][1000 genomes]
rs4696294	0.81[EUR][1000 genomes]
rs55668815	0.86[EUR][1000 genomes]
rs6535809	1.00[CEU][hapmap];0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6535811	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6535812	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6535813	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6535814	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6535815	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6535817	0.96[CEU][hapmap];0.82[CHB][hapmap];0.90[EUR][1000 genomes]
rs6535818	1.00[CEU][hapmap];0.82[CHB][hapmap];0.82[GIH][hapmap];0.87[MEX][hapmap];0.86[TSI][hapmap];0.85[EUR][1000 genomes]
rs6535819	1.00[CEU][hapmap];0.82[CHB][hapmap];0.82[GIH][hapmap];0.83[MEX][hapmap];0.86[TSI][hapmap];0.88[EUR][1000 genomes]
rs6535821	0.89[CEU][hapmap];0.82[EUR][1000 genomes]
rs6810860	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.95[TSI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6817058	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6817586	1.00[CEU][hapmap];0.82[CHB][hapmap];0.89[EUR][1000 genomes]
rs6818667	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6823002	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6823194	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6823421	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6823423	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6823462	0.83[EUR][1000 genomes]
rs6825241	0.80[EUR][1000 genomes]
rs6832562	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6833368	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6834095	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.95[TSI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6838966	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.95[TSI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6839074	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6840360	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6840678	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.93[TSI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6841204	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6841783	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6845944	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6846114	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.91[TSI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6849050	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.89[MKK][hapmap];0.93[TSI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7439465	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs749982	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs751012	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs751014	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7663045	1.00[CEU][hapmap];0.82[CHB][hapmap];0.86[EUR][1000 genomes]
rs7667197	0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7669465	0.80[GIH][hapmap]
rs7669761	0.82[GIH][hapmap]
rs7669977	1.00[CEU][hapmap];0.82[CHB][hapmap];0.82[GIH][hapmap];0.83[MEX][hapmap];0.86[TSI][hapmap];0.86[EUR][1000 genomes]
rs7671651	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7684350	1.00[CEU][hapmap];0.82[CHB][hapmap];0.86[EUR][1000 genomes]
rs7695162	0.92[EUR][1000 genomes]
rs907237	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9307887	0.83[EUR][1000 genomes]
rs9995704	0.85[EUR][1000 genomes]
rs9998462	0.88[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	esv2755535	chr4:152549395-152609395	Enhancers Weak transcription Genic enhancers Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv4551	chr4:152582617-152627367	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv1026511	chr4:152593382-152611915	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs1896883	PET112L	cis	multi-tissue	Pritchard
rs1896883	PET112L	cis	parietal	SCAN
rs1896883	PET112L	cis	Lymphoblastoid	GTEx
rs1896883	FAM160A1	cis	cerebellum	SCAN
rs1896883	SH3D19	cis	cerebellum	SCAN
rs1896883	PET112L	cis	lymphoblastoid	seeQTL
rs1896883	PET112L	cis	cerebellum	SCAN

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:152563800-152625200	Weak transcription	Hela-S3	cervix
2	chr4:152567400-152608600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
3	chr4:152567800-152609000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr4:152579200-152597400	Weak transcription	Liver	Liver
5	chr4:152580200-152596000	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr4:152580800-152595800	Weak transcription	HUES6 Cell Line	embryonic stem cell
7	chr4:152580800-152596800	Weak transcription	Primary T cells from cord blood	blood
8	chr4:152581200-152602800	Weak transcription	Primary T helper cells fromperipheralblood	blood
9	chr4:152581200-152608400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
10	chr4:152581800-152595600	Weak transcription	Duodenum Smooth Muscle	Duodenum
11	chr4:152582400-152595800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr4:152583200-152596000	Weak transcription	Spleen	Spleen
13	chr4:152584600-152595400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr4:152584800-152595800	Weak transcription	Fetal Intestine Large	intestine
15	chr4:152585200-152596000	Weak transcription	Colonic Mucosa	Colon
16	chr4:152585600-152628600	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr4:152585800-152596200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr4:152585800-152600400	Weak transcription	Gastric	stomach
19	chr4:152585800-152640400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
20	chr4:152586000-152596600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
21	chr4:152586400-152609000	Weak transcription	Primary hematopoietic stem cells	blood
22	chr4:152588400-152596000	Weak transcription	Brain Germinal Matrix	brain
23	chr4:152588800-152595800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr4:152589200-152608800	Weak transcription	Primary T cells fromperipheralblood	blood
25	chr4:152589200-152619200	Weak transcription	Dnd41	blood
26	chr4:152590000-152595800	Weak transcription	Brain Anterior Caudate	brain
27	chr4:152590000-152595800	Weak transcription	Brain Inferior Temporal Lobe	brain
28	chr4:152590200-152595400	Weak transcription	Psoas Muscle	Psoas
29	chr4:152590200-152596000	Weak transcription	HSMMtube	muscle
30	chr4:152590400-152595400	Weak transcription	Brain Substantia Nigra	brain
31	chr4:152590400-152595600	Weak transcription	HUES64 Cell Line	embryonic stem cell
32	chr4:152590400-152601600	Weak transcription	Primary B cells from cord blood	blood
33	chr4:152590600-152595800	Weak transcription	Brain Cingulate Gyrus	brain
34	chr4:152590600-152595800	Weak transcription	Fetal Kidney	kidney
35	chr4:152590600-152597600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr4:152590600-152609000	Weak transcription	Primary monocytes fromperipheralblood	blood
37	chr4:152590800-152596000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr4:152591200-152596000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr4:152591200-152597400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr4:152591200-152608600	Weak transcription	Primary T helper cells PMA-I stimulated	--
41	chr4:152591200-152646800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
42	chr4:152591400-152595800	Weak transcription	Rectal Mucosa Donor 29	rectum
43	chr4:152591800-152596000	Enhancers	Fetal Heart	heart
44	chr4:152592000-152595800	Weak transcription	HUES48 Cell Line	embryonic stem cell
45	chr4:152592000-152598200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr4:152592200-152596000	Enhancers	Right Ventricle	heart
47	chr4:152592200-152608000	Weak transcription	Thymus	Thymus
48	chr4:152592400-152597800	Enhancers	Left Ventricle	heart
49	chr4:152592600-152595400	Weak transcription	Rectal Mucosa Donor 31	rectum
50	chr4:152592600-152595800	Enhancers	Right Atrium	heart

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links