Variant report

Variant	rs6490284
Chromosome Location	chr12:120526760-120526761
allele	A/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:7)
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	BCL3	chr12:120526717-120527332	A549	lung:	n/a	n/a
2	POLR2A	chr12:120526746-120527297	PFSK-1	brain:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:120524872..120526862-chr12:120728352..120730035,2	K562	blood:
2	chr12:120523806..120527797-chr12:120636547..120640278,4	K562	blood:
3	chr12:120522807..120526781-chr12:120552984..120555977,5	MCF-7	breast:
4	chr12:120524977..120526839-chr12:120528697..120530517,2	MCF-7	breast:
5	chr12:120524817..120526955-chr12:120527909..120530871,2	K562	blood:
6	chr12:120525354..120527511-chr12:120632416..120635018,2	MCF-7	breast:
7	chr12:120524045..120526996-chr12:120539011..120541039,3	MCF-7	breast:

No data

Variant related genes	Relation type
CCDC64	TF binding region
ENSG00000089154	Chromatin interaction
ENSG00000111737	Chromatin interaction
ENSG00000089157	Chromatin interaction
ENSG00000202538	Chromatin interaction
ENSG00000255857	Chromatin interaction
ENSG00000135127	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10744747	0.83[ASN][1000 genomes]
rs10849732	0.92[CEU][hapmap];0.82[TSI][hapmap]
rs11064986	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11064998	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11065004	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11065014	0.82[ASW][hapmap];0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11065017	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11065018	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12311327	0.88[ASW][hapmap];0.92[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.93[TSI][hapmap];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12320072	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2239200	0.83[CHB][hapmap]
rs2239201	0.83[CHB][hapmap]
rs2240311	0.94[ASW][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2393570	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2893812	0.91[CHB][hapmap];0.91[CHD][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs3742044	0.91[CHB][hapmap];0.86[JPT][hapmap];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3759399	0.97[ASN][1000 genomes]
rs3852586	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3852588	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3886910	0.92[CEU][hapmap];0.91[CHB][hapmap];0.85[JPT][hapmap];0.83[ASN][1000 genomes]
rs3999575	0.98[ASN][1000 genomes]
rs4105713	0.85[EUR][1000 genomes]
rs4351876	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4767870	0.82[ASN][1000 genomes]
rs4767873	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6490278	0.88[ASW][hapmap];0.92[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];0.86[JPT][hapmap];0.98[MKK][hapmap];0.96[TSI][hapmap];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6490280	0.84[EUR][1000 genomes]
rs6490281	0.92[CEU][hapmap];1.00[GIH][hapmap];0.96[TSI][hapmap];0.85[EUR][1000 genomes]
rs6490283	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7295717	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7300023	0.83[CHB][hapmap]
rs7302874	0.92[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs7304325	0.88[ASW][hapmap];0.92[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];0.86[JPT][hapmap];0.94[MKK][hapmap];0.90[TSI][hapmap]
rs7305625	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7306739	0.88[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.98[MKK][hapmap];0.96[TSI][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7312811	0.88[ASW][hapmap];0.92[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];0.86[JPT][hapmap];0.98[MKK][hapmap];0.96[TSI][hapmap];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7314959	0.88[ASW][hapmap];0.85[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[MKK][hapmap];0.96[TSI][hapmap];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7956436	0.95[CHB][hapmap];0.86[JPT][hapmap];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7958497	0.86[GIH][hapmap]
rs7960725	0.88[ASW][hapmap];0.92[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.98[MKK][hapmap];0.96[TSI][hapmap];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7961738	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7962812	0.88[ASW][hapmap];0.92[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];0.86[JPT][hapmap];0.98[MKK][hapmap];0.96[TSI][hapmap];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7965829	0.83[CHB][hapmap]
rs7971249	0.85[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7977281	0.92[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];0.86[JPT][hapmap];0.96[TSI][hapmap];0.83[ASN][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	esv3525916	chr12:120345352-120665045	Bivalent Enhancer Genic enhancers Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	99 gene(s)	inside rSNPs	diseases
2	esv3525917	chr12:120345352-120665045	Weak transcription Enhancers Genic enhancers Active TSS Bivalent/Poised TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	99 gene(s)	inside rSNPs	diseases
3	nsv899555	chr12:120519124-120840522	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	499 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6490284	GATC	cis	lymphoblastoid	seeQTL

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:120518200-120528600	Weak transcription	Gastric	stomach
2	chr12:120524800-120531000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr12:120525000-120530400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr12:120525400-120527200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr12:120525400-120527600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr12:120525400-120527800	Weak transcription	Spleen	Spleen
7	chr12:120525400-120528200	Weak transcription	Psoas Muscle	Psoas
8	chr12:120525400-120528400	Weak transcription	Esophagus	oesophagus
9	chr12:120525400-120528800	Weak transcription	Lung	lung
10	chr12:120525400-120529600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr12:120525400-120529800	Weak transcription	Fetal Intestine Large	intestine
12	chr12:120525400-120530200	Weak transcription	Left Ventricle	heart
13	chr12:120525400-120534200	Weak transcription	Right Atrium	heart
14	chr12:120525600-120527000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr12:120525600-120527400	Weak transcription	Thymus	Thymus
16	chr12:120525600-120527600	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr12:120525600-120527600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
18	chr12:120525600-120527600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr12:120525600-120527600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
20	chr12:120525600-120527600	Weak transcription	Fetal Brain Female	brain
21	chr12:120525600-120527600	Weak transcription	Fetal Muscle Trunk	muscle
22	chr12:120525600-120527600	Weak transcription	Placenta	Placenta
23	chr12:120525600-120528000	Weak transcription	HUES48 Cell Line	embryonic stem cell
24	chr12:120525600-120528000	Weak transcription	Cortex derived primary cultured neurospheres	brain
25	chr12:120525600-120528000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr12:120525600-120528200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr12:120525600-120528600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr12:120525600-120528600	Weak transcription	Pancreas	Pancrea
29	chr12:120525600-120529000	Weak transcription	Stomach Smooth Muscle	stomach
30	chr12:120525600-120529200	Weak transcription	Muscle Satellite Cultured Cells	--
31	chr12:120525600-120529200	Weak transcription	Fetal Intestine Small	intestine
32	chr12:120525600-120529400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr12:120525600-120529400	Weak transcription	Fetal Stomach	stomach
34	chr12:120525600-120529400	Weak transcription	HSMM	muscle
35	chr12:120525600-120529400	Weak transcription	NHLF	lung
36	chr12:120525600-120529600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
37	chr12:120525600-120529600	Weak transcription	Sigmoid Colon	Sigmoid Colon
38	chr12:120525600-120529800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr12:120525600-120529800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
40	chr12:120525600-120530000	Weak transcription	Adipose Nuclei	Adipose
41	chr12:120525600-120530000	Weak transcription	Brain Substantia Nigra	brain
42	chr12:120525600-120530200	Weak transcription	Colonic Mucosa	Colon
43	chr12:120525600-120530200	Weak transcription	Right Ventricle	heart
44	chr12:120525600-120530400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr12:120525600-120530400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr12:120525600-120530400	Weak transcription	Brain Hippocampus Middle	brain
47	chr12:120525600-120531200	Weak transcription	Fetal Lung	lung
48	chr12:120525600-120531400	Weak transcription	Placenta Amnion	Placenta Amnion
49	chr12:120525600-120531600	Weak transcription	Aorta	Aorta
50	chr12:120525600-120531600	Weak transcription	Brain Angular Gyrus	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links