Variant report

Variant	rs12489984
Chromosome Location	chr3:150863514-150863515
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:150480168..150482744-chr3:150863449..150865397,2	MCF-7	breast:
2	chr3:150834592..150835523-chr3:150863486..150864448,3	MCF-7	breast:
3	chr3:150726245..150727142-chr3:150863441..150864471,12	MCF-7	breast:
4	chr3:150803865..150806747-chr3:150863214..150865555,2	MCF-7	breast:
5	chr3:150726303..150727160-chr3:150863474..150864399,6	MCF-7	breast:
6	chr3:150643163..150644188-chr3:150863256..150864452,7	MCF-7	breast:
7	chr3:150859764..150861987-chr3:150862160..150864120,2	MCF-7	breast:
8	chr3:150784607..150785620-chr3:150863485..150864424,9	MCF-7	breast:
9	chr3:150643602..150644107-chr3:150863509..150864363,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000181788	Chromatin interaction
ENSG00000144893	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs1003246	0.87[EUR][1000 genomes]
rs1005726	0.88[EUR][1000 genomes]
rs10755104	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10935825	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10935827	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10935828	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11914598	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11919212	0.85[EUR][1000 genomes]
rs13434276	0.88[ASN][1000 genomes]
rs1346943	0.90[ASN][1000 genomes]
rs1431492	0.86[EUR][1000 genomes]
rs1431493	0.87[EUR][1000 genomes]
rs16863172	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1835668	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1897296	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs1920392	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2014240	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2060081	0.88[EUR][1000 genomes]
rs28594277	0.81[EUR][1000 genomes]
rs28690162	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3773615	0.87[EUR][1000 genomes]
rs3915228	0.87[EUR][1000 genomes]
rs61184267	0.87[EUR][1000 genomes]
rs6414377	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6440721	0.85[EUR][1000 genomes]
rs6765294	0.85[EUR][1000 genomes]
rs6767918	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6772640	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6780120	0.87[EUR][1000 genomes]
rs6787683	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6790661	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6800064	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6801591	0.87[EUR][1000 genomes]
rs7427471	0.87[EUR][1000 genomes]
rs747205	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7633492	0.85[EUR][1000 genomes]
rs7645665	0.83[EUR][1000 genomes]
rs9289832	0.84[EUR][1000 genomes]
rs965843	0.86[ASN][1000 genomes]
rs9683109	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs970235	0.90[ASN][1000 genomes]
rs9813224	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9822304	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9823077	0.88[EUR][1000 genomes]
rs9848163	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9850016	0.90[ASN][1000 genomes]
rs9876500	0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv829756	chr3:150692636-150889738	Weak transcription Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv460894	chr3:150770614-151095093	Enhancers Flanking Bivalent TSS/Enh Weak transcription Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	nsv592045	chr3:150770614-151095093	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
4	esv2757897	chr3:150791625-150957485	ZNF genes & repeats Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	esv2759188	chr3:150791625-150957485	Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	nsv877648	chr3:150792444-150895145	Enhancers Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:150826400-150863600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr3:150827400-150873000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr3:150844800-150863600	Weak transcription	Brain Angular Gyrus	brain
4	chr3:150844800-150863600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
5	chr3:150846400-150863600	Weak transcription	Brain Anterior Caudate	brain
6	chr3:150859600-150863600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr3:150861200-150863600	Enhancers	Primary hematopoietic stem cells	blood
8	chr3:150861200-150865000	Enhancers	Primary hematopoietic stem cells short term culture	blood
9	chr3:150861400-150863600	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr3:150861400-150872600	Weak transcription	Cortex derived primary cultured neurospheres	brain
11	chr3:150861600-150863600	Weak transcription	Fetal Lung	lung
12	chr3:150861600-150863600	Weak transcription	Fetal Muscle Leg	muscle
13	chr3:150861800-150864000	Weak transcription	Fetal Kidney	kidney
14	chr3:150861800-150872600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr3:150862000-150863600	Enhancers	iPS-20b Cell Line	embryonic stem cell
16	chr3:150862000-150872200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr3:150862200-150864000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr3:150862400-150864200	Enhancers	iPS-15b Cell Line	embryonic stem cell
19	chr3:150862600-150863600	Weak transcription	Fetal Thymus	thymus
20	chr3:150862600-150864200	Enhancers	HUES48 Cell Line	embryonic stem cell
21	chr3:150862600-150864200	Enhancers	iPS-18 Cell Line	embryonic stem cell
22	chr3:150862600-150864400	Enhancers	ES-I3 Cell Line	embryonic stem cell
23	chr3:150862600-150864400	Enhancers	H1 Cell Line	embryonic stem cell
24	chr3:150862600-150864400	Enhancers	Primary B cells from peripheral blood	blood
25	chr3:150862800-150863600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr3:150862800-150865000	Enhancers	Fetal Intestine Small	intestine
27	chr3:150862800-150873000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr3:150862800-150873600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr3:150863000-150863800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
30	chr3:150863000-150864200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr3:150863000-150864400	Enhancers	HUES6 Cell Line	embryonic stem cell
32	chr3:150863000-150864800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr3:150863200-150864200	Enhancers	HUES64 Cell Line	embryonic stem cell
34	chr3:150863200-150889000	Weak transcription	H9 Cell Line	embryonic stem cell
35	chr3:150863400-150863600	Enhancers	Primary neutrophils fromperipheralblood	blood
36	chr3:150863400-150863800	Bivalent Enhancer	HUVEC	blood vessel
37	chr3:150863400-150864200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
38	chr3:150863400-150864800	Enhancers	Fetal Intestine Large	intestine

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