Variant report

Variant	rs12490471
Chromosome Location	chr3:51535589-51535590
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:2 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr3:51535520-51535670	GM12873	blood:	n/a	n/a
2	CTCF	chr3:51535440-51535590	GM12869	blood:	n/a	n/a

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:51534170..51537061-chr3:51667512..51669238,2	MCF-7	breast:
2	chr3:51534724..51536284-chr3:51571592..51573333,2	MCF-7	breast:
3	chr3:51535498..51537200-chr3:51671383..51672799,10	MCF-7	breast:
4	chr3:51533144..51535964-chr3:51704671..51707377,2	MCF-7	breast:
5	chr3:51533596..51535948-chr3:51713544..51717803,3	K562	blood:
6	chr3:51426988..51429067-chr3:51532869..51536301,5	K562	blood:
7	chr3:51535362..51537106-chr3:51541973..51543494,2	K562	blood:
8	chr3:51535149..51536784-chr3:51671586..51672589,18	MCF-7	breast:
9	chr3:51532744..51536241-chr3:51571123..51575595,5	K562	blood:
10	chr3:51427878..51430154-chr3:51533292..51535600,2	MCF-7	breast:
11	chr3:51532096..51536424-chr3:51702408..51707498,7	K562	blood:
12	chr3:51428575..51432934-chr3:51531325..51537191,8	K562	blood:

No data

Variant related genes	Relation type
VPRBP	TF binding region
ENSG00000179837	Chromatin interaction
ENSG00000164080	Chromatin interaction
ENSG00000164081	Chromatin interaction

Extended variants
information (count: 115 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:114)

rs_ID	r²[population]
rs10510757	0.94[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs10510758	0.86[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs12485610	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12486568	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12487426	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12487468	0.89[CHB][hapmap];0.94[JPT][hapmap];0.89[ASN][1000 genomes]
rs12489414	0.90[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs12490889	0.84[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs12491048	0.92[ASN][1000 genomes]
rs12492624	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12493265	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12493618	0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12493857	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12493978	0.89[CHB][hapmap];0.94[JPT][hapmap];0.89[ASN][1000 genomes]
rs12494462	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12494979	0.90[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs12496340	0.93[EUR][1000 genomes]
rs13089799	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13090348	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13324384	0.87[EUR][1000 genomes]
rs1370124	0.92[ASN][1000 genomes]
rs17051783	0.86[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs17051811	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17661242	0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs17712228	0.89[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs1842394	0.89[CHB][hapmap];0.94[JPT][hapmap];0.81[ASN][1000 genomes]
rs2033703	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2082992	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2082993	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2217938	0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2241785	0.92[ASN][1000 genomes]
rs2304512	0.86[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2306430	0.90[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2306431	0.89[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2356261	0.86[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2356298	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs35536327	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3749317	0.86[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs3792408	0.86[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs3804766	0.86[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs3828395	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs4468966	0.89[CHB][hapmap];0.94[JPT][hapmap];0.84[ASN][1000 genomes]
rs4687553	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4687563	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4687592	0.81[EUR][1000 genomes]
rs4687599	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes]
rs4687601	0.89[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs4687605	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4687610	0.89[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs4687656	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4687691	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4687731	0.87[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs4687769	0.87[EUR][1000 genomes]
rs4687777	0.86[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs4687794	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4687803	0.89[AMR][1000 genomes]
rs4687804	0.81[AMR][1000 genomes]
rs4687811	0.90[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs4687812	0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs4687813	0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs4974096	0.89[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs55667499	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55671465	0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs55706150	0.87[EUR][1000 genomes]
rs55872019	0.81[EUR][1000 genomes]
rs56239081	0.98[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56729479	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs57027950	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs57047724	0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs57603251	0.84[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs57700326	0.81[ASN][1000 genomes]
rs57831708	0.92[ASN][1000 genomes]
rs58059174	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58189274	0.90[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs58201844	0.84[ASN][1000 genomes]
rs58568178	0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs58762652	1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs58836277	0.86[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs59563413	0.88[ASN][1000 genomes]
rs59564034	0.85[AFR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs59838596	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs59953568	0.80[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs60007226	0.85[AFR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs60606339	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61233013	0.97[ASN][1000 genomes]
rs61419317	0.86[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs61689323	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72945708	0.88[ASN][1000 genomes]
rs72945713	0.92[ASN][1000 genomes]
rs72951443	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72951490	0.87[EUR][1000 genomes]
rs7375146	0.87[EUR][1000 genomes]
rs73834252	0.86[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs73834253	0.98[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73834254	0.98[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73834257	0.82[AFR][1000 genomes]
rs73834258	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73834265	0.87[EUR][1000 genomes]
rs73837439	0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs73837442	0.94[ASN][1000 genomes]
rs73837443	0.86[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs751076	0.83[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs7642698	0.82[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs880478	0.90[CHB][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs9817077	0.89[CHB][hapmap];0.94[JPT][hapmap];0.83[ASN][1000 genomes]
rs9817872	0.89[CHB][hapmap];0.94[JPT][hapmap];0.83[ASN][1000 genomes]
rs9819195	0.89[CHB][hapmap];0.94[JPT][hapmap];0.83[ASN][1000 genomes]
rs9820140	0.92[ASN][1000 genomes]
rs9827186	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9829057	0.89[CHB][hapmap];0.94[JPT][hapmap];0.84[ASN][1000 genomes]
rs9842600	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9843583	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9856134	0.89[CHB][hapmap];0.88[JPT][hapmap];0.83[ASN][1000 genomes]
rs9861019	0.91[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	nsv1014464	chr3:51220151-51909780	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:51534600-51535800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr3:51534600-51535800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr3:51534600-51535800	Weak transcription	Fetal Heart	heart
4	chr3:51534600-51536400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
5	chr3:51534800-51535600	Weak transcription	Duodenum Smooth Muscle	Duodenum
6	chr3:51534800-51535600	Enhancers	K562	blood
7	chr3:51534800-51535800	Weak transcription	Primary T cells from cord blood	blood
8	chr3:51534800-51535800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
9	chr3:51534800-51535800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
10	chr3:51534800-51535800	Weak transcription	Brain Angular Gyrus	brain
11	chr3:51534800-51535800	Weak transcription	Brain Anterior Caudate	brain
12	chr3:51534800-51535800	Weak transcription	Brain Cingulate Gyrus	brain
13	chr3:51534800-51535800	Weak transcription	Brain Substantia Nigra	brain
14	chr3:51534800-51535800	Weak transcription	Colon Smooth Muscle	Colon
15	chr3:51534800-51535800	Weak transcription	Fetal Lung	lung
16	chr3:51534800-51535800	Weak transcription	Pancreas	Pancrea
17	chr3:51534800-51535800	Weak transcription	Skeletal Muscle Female	skeletal muscle
18	chr3:51534800-51536000	Weak transcription	HUES6 Cell Line	embryonic stem cell
19	chr3:51534800-51536000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr3:51534800-51536000	Weak transcription	Duodenum Mucosa	Duodenum
21	chr3:51534800-51536000	Weak transcription	Fetal Muscle Trunk	muscle
22	chr3:51534800-51536000	Weak transcription	Fetal Muscle Leg	muscle
23	chr3:51534800-51536000	Weak transcription	Skeletal Muscle Male	skeletal muscle
24	chr3:51534800-51536200	Enhancers	Primary T helper cells PMA-I stimulated	--
25	chr3:51534800-51536200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
26	chr3:51534800-51536200	Enhancers	Dnd41	blood
27	chr3:51534800-51536200	Enhancers	GM12878-XiMat	blood
28	chr3:51534800-51536200	Enhancers	Hela-S3	cervix
29	chr3:51534800-51536400	Enhancers	Primary T cells fromperipheralblood	blood
30	chr3:51534800-51536600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
31	chr3:51534800-51537000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr3:51534800-51537200	Weak transcription	Placenta Amnion	Placenta Amnion
33	chr3:51534800-51538000	Enhancers	Placenta	Placenta
34	chr3:51534800-51539600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
35	chr3:51535000-51536000	Weak transcription	Primary T helper cells fromperipheralblood	blood
36	chr3:51535000-51536000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr3:51535000-51536000	Weak transcription	Rectal Smooth Muscle	rectum
38	chr3:51535000-51536000	Weak transcription	Monocytes-CD14+_RO01746	blood
39	chr3:51535000-51536200	Enhancers	Stomach Smooth Muscle	stomach
40	chr3:51535000-51541400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr3:51535200-51535600	Weak transcription	Primary B cells from peripheral blood	blood
42	chr3:51535200-51535600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
43	chr3:51535200-51535600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
44	chr3:51535200-51535600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
45	chr3:51535200-51535600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
46	chr3:51535200-51535600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
47	chr3:51535200-51535600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
48	chr3:51535200-51535600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr3:51535200-51535600	Weak transcription	Adipose Nuclei	Adipose
50	chr3:51535200-51535600	Weak transcription	Fetal Thymus	thymus

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links