Variant report

Variant	rs12486069
Chromosome Location	chr3:160825648-160825649
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:5)
CpG islands
(count:61)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:5 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GATA3	chr3:160824743-160825770	MCF-7	breast:	n/a	chr3:160825643-160825652
2	CEBPB	chr3:160825588-160825803	HepG2	liver:	n/a	n/a
3	CEBPB	chr3:160825637-160825809	A549	lung:	n/a	n/a
4	ZNF217	chr3:160825013-160825746	MCF-7	breast:	n/a	n/a
5	SIN3AK20	chr3:160824749-160825787	MCF-7	breast:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr3:160825607-160825657	A549	lung:	n/a
2	chr3:160825607-160825657	HRCEpiC	kidney:	n/a
3	chr3:160825607-160825657	SKMC	muscle:	n/a
4	chr3:160825607-160825657	H1-hESC	embryonic stem cell:	embryo
5	chr3:160825607-160825657	HCPEpiC	choroid plexus:	n/a
6	chr3:160825607-160825657	GM19239	blood:	n/a
7	chr3:160825607-160825657	CMK	blood:	n/a
8	chr3:160825607-160825657	HCT-116	colon:	n/a
9	chr3:160825607-160825657	AG10803	skin:	n/a
10	chr3:160825607-160825657	NHDF-neo	bronchial:	n/a
11	chr3:160825607-160825657	ECC-1	luminal epithelium:	n/a
12	chr3:160825607-160825657	SK-N-SH_RA	brain:	n/a
13	chr3:160825607-160825657	T-47D	breast:	n/a
14	chr3:160825607-160825657	HRE	kidney:	n/a
15	chr3:160825607-160825657	AG09309	skin:	n/a
16	chr3:160825607-160825657	GM12878	blood:	n/a
17	chr3:160825607-160825657	BE2_C	brain:	n/a
18	chr3:160825607-160825657	HUVEC	blood vessel:	n/a
19	chr3:160825607-160825657	K562	blood:	n/a
20	chr3:160825607-160825657	HCM	heart:	n/a
21	chr3:160825607-160825657	MCF-7	breast:	n/a
22	chr3:160825607-160825657	HEEpiC	esophagus:	n/a
23	chr3:160825607-160825657	RPTEC	kidney:	n/a
24	chr3:160825607-160825657	AG04450	lung:	fetal
25	chr3:160825607-160825657	GM12892	blood:	n/a
26	chr3:160825607-160825657	AG09319	gingival:	n/a
27	chr3:160825607-160825657	HAEpiC	amniotic membrane:	n/a
28	chr3:160825607-160825657	Caco-2	colon:	n/a
29	chr3:160825607-160825657	PANC-1	pancreas:	n/a
30	chr3:160825607-160825657	HCF	heart:	n/a
31	chr3:160825607-160825657	U87	brain:	n/a
32	chr3:160825607-160825657	HNPCEpiC	eye:	n/a
33	chr3:160825607-160825657	HRPEpiC	eye:	n/a
34	chr3:160825607-160825657	Hepatocyte	liver:	n/a
35	chr3:160825607-160825657	PFSK-1	brain:	n/a
36	chr3:160825607-160825657	HPAEpiC	pulmonary alveolar:	n/a
37	chr3:160825607-160825657	IMR90	lung:	fetal
38	chr3:160825607-160825657	SAEC	small airway:	n/a
39	chr3:160825607-160825657	MCF10A-Er-Src	breast:	n/a
40	chr3:160825607-160825657	HIPEpiC	eye:	n/a
41	chr3:160825607-160825657	AoSMC	blood vessel:	n/a
42	chr3:160825607-160825657	LNCaP	prostate:	n/a
43	chr3:160825607-160825657	Jurkat	blood:	n/a
44	chr3:160825607-160825657	NHBE	bronchial:	n/a
45	chr3:160825607-160825657	AG04449	skin:	fetal
46	chr3:160825607-160825657	NB4	blood:	n/a
47	chr3:160825607-160825657	NT2-D1	testis:	n/a
48	chr3:160825607-160825657	GM06990	blood:	n/a
49	chr3:160825607-160825657	BJ	skin:	n/a
50	chr3:160825607-160825657	SK-N-MC	brain:	n/a

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:160823684..160825879-chr3:160830015..160833205,3	MCF-7	breast:
2	chr3:160824306..160825835-chr3:160990515..160993079,2	MCF-7	breast:
3	chr3:160818503..160825890-chr3:160937051..160945986,18	MCF-7	breast:
4	chr3:160821182..160827138-chr3:160937374..160941314,7	MCF-7	breast:
5	chr3:160824125..160825880-chr3:160827918..160829533,2	K562	blood:
6	chr3:160825465..160827951-chr3:160887384..160889097,2	MCF-7	breast:

No data

Variant related genes	Relation type
B3GALNT1	TF binding region
B3GALNT1	CpG island
ENSG00000169251	Chromatin interaction
ENSG00000271052	Chromatin interaction

Extended variants
information (count: 103 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:96)

rs_ID	r²[population]
rs1017799	0.81[ASN][1000 genomes]
rs12485519	0.83[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs12486103	0.83[AMR][1000 genomes]
rs12489004	0.87[ASN][1000 genomes]
rs12489125	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12490149	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs12493266	0.84[ASN][1000 genomes]
rs12496235	1.00[ASN][1000 genomes]
rs12496837	0.93[AMR][1000 genomes]
rs13315320	0.87[ASN][1000 genomes]
rs13319771	0.87[ASN][1000 genomes]
rs16831799	0.84[ASN][1000 genomes]
rs16831850	1.00[ASN][1000 genomes]
rs16831864	1.00[ASN][1000 genomes]
rs16831882	0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs16831942	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs28451189	0.82[ASN][1000 genomes]
rs28704960	1.00[ASN][1000 genomes]
rs3925722	0.94[ASN][1000 genomes]
rs4296611	0.90[ASN][1000 genomes]
rs4352387	0.87[ASN][1000 genomes]
rs4468992	0.87[ASN][1000 genomes]
rs4580574	0.90[ASN][1000 genomes]
rs4635725	0.84[ASN][1000 genomes]
rs57903480	0.84[ASN][1000 genomes]
rs59567999	0.90[ASN][1000 genomes]
rs59593286	0.88[ASN][1000 genomes]
rs59757775	0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs59776766	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs59867530	0.83[AMR][1000 genomes]
rs60121330	1.00[ASN][1000 genomes]
rs6441350	1.00[ASN][1000 genomes]
rs6441365	0.90[ASN][1000 genomes]
rs6441372	0.87[ASN][1000 genomes]
rs6762064	0.90[ASN][1000 genomes]
rs6771581	0.88[ASN][1000 genomes]
rs6774919	0.90[ASN][1000 genomes]
rs6775446	0.87[ASN][1000 genomes]
rs6775931	0.87[ASN][1000 genomes]
rs6778186	0.87[ASN][1000 genomes]
rs6782415	0.82[ASN][1000 genomes]
rs6782518	0.87[ASN][1000 genomes]
rs6785714	0.87[ASN][1000 genomes]
rs6787447	0.87[ASN][1000 genomes]
rs6790805	0.87[ASN][1000 genomes]
rs6796168	1.00[ASN][1000 genomes]
rs6801664	0.87[ASN][1000 genomes]
rs6805976	0.87[ASN][1000 genomes]
rs73017340	0.87[ASN][1000 genomes]
rs73026933	0.90[ASN][1000 genomes]
rs73026967	0.87[ASN][1000 genomes]
rs73026968	0.87[ASN][1000 genomes]
rs73026983	0.87[ASN][1000 genomes]
rs73026987	0.87[ASN][1000 genomes]
rs73026989	0.87[ASN][1000 genomes]
rs734915	0.83[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs7615833	0.87[ASN][1000 genomes]
rs7615868	0.94[ASN][1000 genomes]
rs7624791	0.87[ASN][1000 genomes]
rs7626773	0.87[ASN][1000 genomes]
rs7627500	0.84[ASN][1000 genomes]
rs7634299	0.87[ASN][1000 genomes]
rs7652624	0.87[ASN][1000 genomes]
rs9290070	0.90[ASN][1000 genomes]
rs9290071	0.84[ASN][1000 genomes]
rs9682249	0.88[ASN][1000 genomes]
rs9682995	0.81[ASN][1000 genomes]
rs9810351	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9812574	0.81[ASN][1000 genomes]
rs9818470	0.87[ASN][1000 genomes]
rs9818835	0.93[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9818992	0.93[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs9819793	0.87[ASN][1000 genomes]
rs9822916	0.87[ASN][1000 genomes]
rs9823424	0.93[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9824535	1.00[ASN][1000 genomes]
rs9824805	0.87[ASN][1000 genomes]
rs9826857	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9830183	1.00[ASN][1000 genomes]
rs9833270	0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs9838945	0.87[ASN][1000 genomes]
rs9841871	0.90[ASN][1000 genomes]
rs9842290	0.87[ASN][1000 genomes]
rs9847842	0.87[ASN][1000 genomes]
rs9851699	0.81[ASN][1000 genomes]
rs9855112	0.94[ASN][1000 genomes]
rs9856742	0.87[ASN][1000 genomes]
rs9858907	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9859641	0.87[ASN][1000 genomes]
rs9862867	0.87[ASN][1000 genomes]
rs9871753	0.90[ASN][1000 genomes]
rs9876077	0.87[ASN][1000 genomes]
rs9877309	0.87[ASN][1000 genomes]
rs9880536	0.84[ASN][1000 genomes]
rs9884100	0.81[ASN][1000 genomes]
rs9985364	0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv931072	chr3:160669567-161159779	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
2	nsv877704	chr3:160806859-160836006	Active TSS Strong transcription Flanking Active TSS Enhancers Weak transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv877705	chr3:160818188-160836006	Flanking Active TSS Enhancers Active TSS Weak transcription Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv877706	chr3:160820175-160826404	Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv877707	chr3:160820175-160836006	Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv877708	chr3:160821969-160826404	Enhancers Active TSS Weak transcription Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
7	nsv877709	chr3:160822198-160826404	Enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:160823200-160832800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr3:160823400-160825800	Weak transcription	Left Ventricle	heart
3	chr3:160823400-160826000	Weak transcription	HMEC	breast
4	chr3:160823400-160826600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr3:160823400-160826600	Weak transcription	HSMM	muscle
6	chr3:160823400-160826800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr3:160823400-160828800	Weak transcription	Fetal Muscle Trunk	muscle
8	chr3:160823400-160829600	Weak transcription	Aorta	Aorta
9	chr3:160823600-160825800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr3:160823600-160826400	Weak transcription	Fetal Stomach	stomach
11	chr3:160823600-160826600	Weak transcription	Duodenum Smooth Muscle	Duodenum
12	chr3:160823600-160828200	Weak transcription	Stomach Smooth Muscle	stomach
13	chr3:160823600-160829200	Weak transcription	Fetal Muscle Leg	muscle
14	chr3:160823800-160826200	Weak transcription	NHDF-Ad	bronchial
15	chr3:160823800-160826600	Weak transcription	NHEK	skin
16	chr3:160823800-160826800	Weak transcription	Brain Angular Gyrus	brain
17	chr3:160823800-160828200	Weak transcription	Right Ventricle	heart
18	chr3:160823800-160830400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
19	chr3:160824000-160827000	Weak transcription	Brain Inferior Temporal Lobe	brain
20	chr3:160824200-160826000	Enhancers	Fetal Heart	heart
21	chr3:160824200-160830800	Weak transcription	Ovary	ovary
22	chr3:160825200-160827000	Enhancers	Primary monocytes fromperipheralblood	blood
23	chr3:160825200-160827200	Enhancers	Monocytes-CD14+_RO01746	blood
24	chr3:160825600-160826200	Enhancers	Primary hematopoietic stem cells short term culture	blood
25	chr3:160825600-160827400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links