Variant report

Variant	rs1870444
Chromosome Location	chr3:48486773-48486774
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:48)
CpG islands
(count:0)
Chromatin interactive
region (count:13)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:48 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:48486745-48487008	K562	blood:	n/a	n/a
2	POLR2A	chr3:48486770-48486984	HCT-116	colon:	n/a	n/a
3	POLR2A	chr3:48486757-48487062	H1-hESC	embryonic stem cell:	n/a	n/a
4	POLR2A	chr3:48486671-48487101	ECC-1	luminal epithelium:	n/a	n/a
5	POLR2A	chr3:48486687-48487003	Hela-S3	cervix:	n/a	n/a
6	POLR2A	chr3:48485860-48488666	GM12891	blood:	n/a	n/a
7	POLR2A	chr3:48486696-48486901	HUVEC	blood vessel:	n/a	n/a
8	POLR2A	chr3:48485350-48488730	PFSK-1	brain:	n/a	n/a
9	POLR2A	chr3:48486507-48487435	PANC-1	pancreas:	n/a	n/a
10	POLR2A	chr3:48486721-48487032	Hela-S3	cervix:	n/a	n/a
11	POLR2A	chr3:48485828-48487191	U87	brain:	n/a	n/a
12	POLR2A	chr3:48485979-48486985	K562	blood:	n/a	n/a
13	POLR2A	chr3:48485975-48487498	MCF10A-Er-Src	breast:	n/a	n/a
14	POLR2A	chr3:48486660-48488714	GM12892	blood:	n/a	n/a
15	POLR2A	chr3:48486720-48486988	SK-N-SH	brain:	n/a	n/a
16	POLR2A	chr3:48486739-48486977	GM12878	blood:	n/a	n/a
17	POLR2A	chr3:48485869-48487078	PANC-1	pancreas:	n/a	n/a
18	POLR2A	chr3:48486692-48487265	U87	brain:	n/a	n/a
19	POLR2A	chr3:48485860-48487052	HUVEC	blood vessel:	n/a	n/a
20	POLR2A	chr3:48486736-48486811	ProgFib	skin:	n/a	n/a
21	MTA3	chr3:48485674-48488326	GM12878	blood:	n/a	n/a
22	POLR2A	chr3:48485480-48488528	SK-N-MC	brain:	n/a	n/a
23	POLR2A	chr3:48486670-48486958	GM12891	blood:	n/a	n/a
24	POLR2A	chr3:48485793-48487443	Hela-S3	cervix:	n/a	n/a
25	POLR2A	chr3:48485560-48487612	PFSK-1	brain:	n/a	n/a
26	POLR2A	chr3:48485869-48488641	SK-N-SH	brain:	n/a	n/a
27	POLR2A	chr3:48485898-48488594	GM12878	blood:	n/a	n/a
28	POLR2A	chr3:48485436-48488575	GM12892	blood:	n/a	n/a
29	POLR2A	chr3:48486668-48487265	U87	brain:	n/a	n/a
30	POLR2A	chr3:48485870-48488879	K562	blood:	n/a	n/a
31	POLR2A	chr3:48485493-48489452	HepG2	liver:	n/a	n/a
32	POLR2A	chr3:48486550-48487119	GM12878	blood:	n/a	n/a
33	NFATC1	chr3:48486686-48487071	GM12878	blood:	n/a	n/a
34	POLR2A	chr3:48485778-48488613	GM12891	blood:	n/a	n/a
35	POLR2A	chr3:48486750-48487032	K562	blood:	n/a	n/a
36	POLR2A	chr3:48486588-48488643	GM12892	blood:	n/a	n/a
37	POLR2A	chr3:48486647-48488468	GM12891	blood:	n/a	n/a
38	POLR2A	chr3:48486741-48487091	GM12892	blood:	n/a	n/a
39	POLR2A	chr3:48486518-48487072	HUVEC	blood vessel:	n/a	n/a
40	POLR2A	chr3:48485586-48487509	K562	blood:	n/a	n/a
41	POLR2A	chr3:48485446-48488566	GM12878	blood:	n/a	n/a
42	MTA3	chr3:48486749-48487108	GM12878	blood:	n/a	n/a
43	POLR2A	chr3:48485914-48488417	GM12878	blood:	n/a	n/a
44	POLR2A	chr3:48486583-48487311	MCF-7	breast:	n/a	n/a
45	POLR2A	chr3:48486677-48486959	HCT-116	colon:	n/a	n/a
46	POLR2A	chr3:48485851-48488721	HUVEC	blood vessel:	n/a	n/a
47	POLR2A	chr3:48485794-48487197	U87	brain:	n/a	n/a
48	POLR2A	chr3:48485947-48488432	MCF10A-Er-Src	breast:	n/a	n/a

No data

(count:13 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:48469445..48473059-chr3:48486174..48489531,5	MCF-7	breast:
2	chr15:42263480..42264426-chr3:48486566..48487176,2	NB4	blood:
3	chr3:48485232..48487898-chr3:48541366..48542951,2	K562	blood:
4	chr3:48460976..48462671-chr3:48486369..48489165,2	MCF-7	breast:
5	chr3:48477555..48484761-chr3:48484855..48490000,13	MCF-7	breast:
6	chr3:48468360..48471756-chr3:48485148..48489754,5	K562	blood:
7	chr3:48486334..48488063-chr3:48594171..48595954,2	MCF-7	breast:
8	chr3:48485967..48488247-chr3:48600373..48602900,2	MCF-7	breast:
9	chr3:48486214..48489756-chr3:48493754..48497547,4	K562	blood:
10	chr3:48484123..48488497-chr3:48591865..48597132,6	K562	blood:
11	chr3:48485548..48495296-chr3:48503776..48510303,13	MCF-7	breast:
12	chr3:48486535..48489941-chr3:48491977..48496128,7	MCF-7	breast:
13	chr3:48228273..48230987-chr3:48484727..48487110,2	K562	blood:

No data

Variant related genes	Relation type
CCDC51	TF binding region
ATRIP	TF binding region
ENSG00000114268	Chromatin interaction
ENSG00000164050	Chromatin interaction
ENSG00000114270	Chromatin interaction
ENSG00000213689	Chromatin interaction
ENSG00000164053	Chromatin interaction
ENSG00000164045	Chromatin interaction
ENSG00000164051	Chromatin interaction
ENSG00000164054	Chromatin interaction
ENSG00000145040	Chromatin interaction
ENSG00000232112	Chromatin interaction

Extended variants
information (count: 94 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:90)

rs_ID	r²[population]
rs1037773	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10470686	0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1109227	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11130170	0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11130171	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11712561	0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11797	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12487542	0.92[EUR][1000 genomes]
rs13069724	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13071337	0.92[EUR][1000 genomes]
rs13072012	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13076076	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13091785	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13314659	0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13324374	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1459242	0.87[EUR][1000 genomes]
rs1459249	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1459250	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1563736	0.92[EUR][1000 genomes]
rs1824363	0.97[ASN][1000 genomes]
rs1975844	0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2045554	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2242150	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2279077	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2290822	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2362450	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2362452	0.87[EUR][1000 genomes]
rs28824259	0.92[EUR][1000 genomes]
rs2885509	0.87[EUR][1000 genomes]
rs2885510	0.87[EUR][1000 genomes]
rs3214041	0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs34761139	0.92[EUR][1000 genomes]
rs35215722	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3774808	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4490383	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4858793	0.87[EUR][1000 genomes]
rs4858795	0.80[AMR][1000 genomes]
rs4858817	0.87[EUR][1000 genomes]
rs60512868	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6442116	0.86[EUR][1000 genomes]
rs6442117	0.89[EUR][1000 genomes]
rs6442118	0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6442119	0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6442120	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6442123	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6442124	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6764415	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6770470	0.92[EUR][1000 genomes]
rs6776700	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6779262	0.87[EUR][1000 genomes]
rs6784322	0.90[EUR][1000 genomes]
rs6784541	0.90[EUR][1000 genomes]
rs6794875	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6796491	0.92[EUR][1000 genomes]
rs6800475	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6804774	0.92[EUR][1000 genomes]
rs6810060	0.91[EUR][1000 genomes]
rs7126	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs725309	0.87[EUR][1000 genomes]
rs725310	0.87[EUR][1000 genomes]
rs73074358	0.92[EUR][1000 genomes]
rs7618883	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7630741	0.89[EUR][1000 genomes]
rs7634377	0.90[EUR][1000 genomes]
rs7635522	0.81[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs7636044	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7636782	0.82[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs7639743	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7653691	0.88[EUR][1000 genomes]
rs898225	0.87[EUR][1000 genomes]
rs922075	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9311423	0.90[EUR][1000 genomes]
rs9311424	0.90[EUR][1000 genomes]
rs9809843	0.92[EUR][1000 genomes]
rs9812647	0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9815103	0.88[EUR][1000 genomes]
rs9817615	0.97[ASN][1000 genomes]
rs9826195	0.92[EUR][1000 genomes]
rs9826247	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9838618	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9849509	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9862575	0.92[EUR][1000 genomes]
rs9864371	0.92[EUR][1000 genomes]
rs9864815	0.92[EUR][1000 genomes]
rs9875280	0.92[EUR][1000 genomes]
rs9876781	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9876891	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9881491	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9883759	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9883927	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv834683	chr3:48301504-48493261	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
2	nsv834684	chr3:48385699-48589323	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
3	nsv590242	chr3:48433635-48556339	Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
4	nsv876761	chr3:48464968-48496758	Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Strong transcription Genic enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	58 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1870444	TMA7	cis	Muscle Skeletal	GTEx
rs1870444	TREX1	Cis_1M	lymphoblastoid	RTeQTL
rs1870444	RP11-24C3.2	cis	Muscle Skeletal	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:48482600-48487200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr3:48482600-48487200	Weak transcription	Right Atrium	heart
3	chr3:48482600-48487400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr3:48482600-48487600	Weak transcription	Ovary	ovary
5	chr3:48483200-48487200	Weak transcription	Rectal Smooth Muscle	rectum
6	chr3:48483400-48487200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr3:48483400-48487200	Weak transcription	Brain Angular Gyrus	brain
8	chr3:48483400-48487400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr3:48483400-48487600	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr3:48483600-48487000	Strong transcription	Brain Germinal Matrix	brain
11	chr3:48483600-48487000	Weak transcription	Fetal Heart	heart
12	chr3:48483600-48487000	Weak transcription	NHDF-Ad	bronchial
13	chr3:48483600-48487200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr3:48483600-48487200	Weak transcription	Fetal Brain Male	brain
15	chr3:48483600-48487200	Strong transcription	Fetal Muscle Leg	muscle
16	chr3:48483600-48487200	Strong transcription	Fetal Stomach	stomach
17	chr3:48483600-48487400	Weak transcription	Psoas Muscle	Psoas
18	chr3:48483600-48487400	Weak transcription	Stomach Mucosa	stomach
19	chr3:48483800-48486800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr3:48483800-48486800	Strong transcription	Cortex derived primary cultured neurospheres	brain
21	chr3:48483800-48486800	Strong transcription	Fetal Brain Female	brain
22	chr3:48483800-48487000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr3:48483800-48487000	Weak transcription	NHEK	skin
24	chr3:48483800-48487200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
25	chr3:48483800-48487200	Weak transcription	Small Intestine	intestine
26	chr3:48483800-48487400	Weak transcription	Placenta Amnion	Placenta Amnion
27	chr3:48484400-48486800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
28	chr3:48484400-48487000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
29	chr3:48484400-48487200	Weak transcription	H9 Cell Line	embryonic stem cell
30	chr3:48484400-48487200	Weak transcription	K562	blood
31	chr3:48484600-48487200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr3:48484600-48487200	Weak transcription	Colonic Mucosa	Colon
33	chr3:48484800-48487200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
34	chr3:48484800-48487400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
35	chr3:48485000-48486800	Weak transcription	HepG2	liver
36	chr3:48485000-48487200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
37	chr3:48485200-48486800	Weak transcription	Primary B cells from cord blood	blood
38	chr3:48485200-48487200	Weak transcription	H1 Cell Line	embryonic stem cell
39	chr3:48485200-48487200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
40	chr3:48485200-48487200	Weak transcription	Fetal Lung	lung
41	chr3:48485200-48487200	Weak transcription	HSMMtube	muscle
42	chr3:48485200-48487400	Weak transcription	Right Ventricle	heart
43	chr3:48485800-48486800	Weak transcription	Hela-S3	cervix
44	chr3:48485800-48487200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
45	chr3:48485800-48487200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr3:48485800-48487200	Weak transcription	HSMM	muscle
47	chr3:48486000-48487000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr3:48486000-48487200	Weak transcription	Primary hematopoietic stem cells	blood
49	chr3:48486000-48487200	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr3:48486000-48487200	Weak transcription	Duodenum Smooth Muscle	Duodenum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links