Variant report

Variant	rs12899246
Chromosome Location	chr15:73423022-73423023
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:73421059..73423677-chr15:73433807..73436410,2	MCF-7	breast:
2	chr15:73075421..73077662-chr15:73422538..73424513,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000260898	Chromatin interaction
ENSG00000259691	Chromatin interaction
ENSG00000159322	Chromatin interaction

Extended variants
information (count: 77 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs10048053	0.83[ASN][1000 genomes]
rs10467949	1.00[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11072406	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1131854	0.81[CEU][hapmap];0.89[CHB][hapmap]
rs11632639	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs11636241	0.81[CEU][hapmap];0.89[CHB][hapmap]
rs11639213	0.81[CEU][hapmap];0.89[CHB][hapmap]
rs11856922	0.94[ASN][1000 genomes]
rs12050848	0.83[CEU][hapmap];0.94[CHB][hapmap];0.89[JPT][hapmap];0.83[ASN][1000 genomes]
rs12708506	0.81[CEU][hapmap];0.89[CHB][hapmap];0.89[JPT][hapmap];0.81[ASN][1000 genomes]
rs12902768	0.83[EUR][1000 genomes]
rs12907139	0.81[CEU][hapmap];0.89[CHB][hapmap];0.94[JPT][hapmap];0.82[ASN][1000 genomes]
rs12916928	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1479337	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1479340	0.83[CHB][hapmap];0.84[ASN][1000 genomes]
rs1564345	0.83[CHB][hapmap];0.83[JPT][hapmap];0.81[ASN][1000 genomes]
rs17762516	0.83[ASN][1000 genomes]
rs17829836	0.84[ASN][1000 genomes]
rs1871385	0.83[CHB][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2010793	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2046017	0.81[CEU][hapmap];0.94[CHB][hapmap];0.83[JPT][hapmap];0.83[ASN][1000 genomes]
rs2127277	0.83[CHB][hapmap];0.83[JPT][hapmap];0.84[ASN][1000 genomes]
rs2251205	0.94[CHB][hapmap];0.89[JPT][hapmap];0.82[ASN][1000 genomes]
rs2415147	0.84[CHB][hapmap]
rs28481558	0.94[ASN][1000 genomes]
rs28743094	0.94[ASN][1000 genomes]
rs28842482	0.96[ASN][1000 genomes]
rs2899784	0.83[ASN][1000 genomes]
rs35060813	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35450875	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3736510	0.83[CHB][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3743489	0.89[CHB][hapmap]
rs3784793	0.84[CHB][hapmap];0.88[JPT][hapmap];0.82[ASN][1000 genomes]
rs4132535	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs4132536	0.83[JPT][hapmap]
rs4777582	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs4777583	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4777589	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs4777590	0.83[JPT][hapmap]
rs4777591	0.94[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs56157337	0.82[ASN][1000 genomes]
rs58060856	0.86[ASN][1000 genomes]
rs62017779	0.83[ASN][1000 genomes]
rs6416501	0.94[ASN][1000 genomes]
rs6416502	0.94[ASN][1000 genomes]
rs6495047	0.94[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs7164894	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs7168555	0.81[CHB][hapmap]
rs7169083	0.83[ASN][1000 genomes]
rs7172021	0.83[CHB][hapmap];0.83[JPT][hapmap];0.87[ASN][1000 genomes]
rs7172396	0.83[CHB][hapmap];0.84[JPT][hapmap];0.87[ASN][1000 genomes]
rs7173142	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7175329	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs747872	0.84[CHB][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs747873	0.82[CHB][hapmap];0.81[AMR][1000 genomes]
rs7495458	0.94[ASN][1000 genomes]
rs8024575	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs8026579	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs8027588	0.81[CEU][hapmap];0.89[CHB][hapmap]
rs8029106	0.83[ASN][1000 genomes]
rs8035063	0.82[ASN][1000 genomes]
rs8042700	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs922516	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs9672588	0.89[CHB][hapmap]
rs9806496	0.83[ASN][1000 genomes]
rs9920186	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3352103	chr15:73191535-73454001	Bivalent/Poised TSS Active TSS Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv482421	chr15:73279141-73426897	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
3	nsv904338	chr15:73313691-73483718	Enhancers Active TSS Strong transcription ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv517966	chr15:73349633-73488753	Enhancers Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv525462	chr15:73349633-73563495	Genic enhancers Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	nsv904339	chr15:73375847-73483718	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv904340	chr15:73375847-73524629	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
8	nsv904341	chr15:73390790-73483718	ZNF genes & repeats Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
9	nsv904342	chr15:73390790-73524629	Enhancers ZNF genes & repeats Strong transcription Weak transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
10	nsv904343	chr15:73396760-73775043	Strong transcription Bivalent Enhancer Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Genic enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
11	nsv527236	chr15:73421239-73469535	Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:73388800-73431200	Weak transcription	Rectal Smooth Muscle	rectum
2	chr15:73396400-73444600	Weak transcription	Psoas Muscle	Psoas
3	chr15:73400400-73434200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr15:73401200-73428200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
5	chr15:73401400-73480200	Weak transcription	Right Ventricle	heart
6	chr15:73403000-73443400	Weak transcription	Fetal Kidney	kidney
7	chr15:73404200-73425800	Weak transcription	Small Intestine	intestine
8	chr15:73404200-73442600	Weak transcription	Left Ventricle	heart
9	chr15:73406600-73423200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr15:73406600-73425200	Weak transcription	HUES48 Cell Line	embryonic stem cell
11	chr15:73406600-73432600	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr15:73407400-73431600	Weak transcription	Duodenum Smooth Muscle	Duodenum
13	chr15:73408000-73443400	Weak transcription	Adipose Nuclei	Adipose
14	chr15:73408800-73424600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr15:73409200-73429200	Weak transcription	Esophagus	oesophagus
16	chr15:73410600-73434600	Weak transcription	Liver	Liver
17	chr15:73410800-73431400	Weak transcription	Colon Smooth Muscle	Colon
18	chr15:73413200-73437200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr15:73413400-73434200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr15:73413600-73446400	Weak transcription	Stomach Smooth Muscle	stomach
21	chr15:73414000-73428200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
22	chr15:73414000-73437000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr15:73414000-73440000	Weak transcription	Fetal Brain Female	brain
24	chr15:73414200-73428600	Weak transcription	Brain Inferior Temporal Lobe	brain
25	chr15:73414200-73445600	Weak transcription	Brain Substantia Nigra	brain
26	chr15:73414400-73458200	Weak transcription	Colonic Mucosa	Colon
27	chr15:73414600-73436600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr15:73415000-73425400	Strong transcription	Rectal Mucosa Donor 31	rectum
29	chr15:73415400-73423800	Weak transcription	Fetal Heart	heart
30	chr15:73415400-73446600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr15:73415600-73428400	Weak transcription	HUES64 Cell Line	embryonic stem cell
32	chr15:73416000-73453200	Weak transcription	Brain Cingulate Gyrus	brain
33	chr15:73416600-73428400	Weak transcription	Fetal Lung	lung
34	chr15:73416600-73444600	Weak transcription	Fetal Muscle Leg	muscle
35	chr15:73416600-73444600	Weak transcription	Lung	lung
36	chr15:73416800-73448800	Weak transcription	Ovary	ovary
37	chr15:73417000-73443000	Weak transcription	Skeletal Muscle Male	skeletal muscle
38	chr15:73417400-73423200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr15:73418200-73433200	Weak transcription	Pancreatic Islets	Pancreatic Islet
40	chr15:73418600-73430600	Weak transcription	Fetal Brain Male	brain
41	chr15:73419400-73428800	Weak transcription	Sigmoid Colon	Sigmoid Colon
42	chr15:73420200-73424800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr15:73420600-73434600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr15:73421000-73443200	Weak transcription	Brain Angular Gyrus	brain
45	chr15:73421400-73433600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
46	chr15:73422200-73423400	Strong transcription	Fetal Intestine Small	intestine
47	chr15:73422200-73424800	Strong transcription	Duodenum Mucosa	Duodenum
48	chr15:73422400-73423400	Strong transcription	Aorta	Aorta
49	chr15:73422400-73423400	Strong transcription	Fetal Intestine Large	intestine
50	chr15:73422400-73423400	Strong transcription	Pancreas	Pancrea

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links