Variant report

Variant	rs754398
Chromosome Location	chr12:57395678-57395679
allele	G/T
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:16)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:16 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:57233430..57234373-chr12:57394911..57395835,6	K562	blood:
2	chr12:57389232..57391365-chr12:57392334..57396255,4	K562	blood:
3	chr12:57119060..57120988-chr12:57393268..57396423,3	K562	blood:
4	chr12:57389602..57391211-chr12:57393734..57396255,2	K562	blood:
5	chr12:57392993..57395915-chr21:44631132..44633606,2	MCF-7	breast:
6	chr12:57395013..57395736-chr20:55745361..55745990,2	MCF-7	breast:
7	chr12:57394373..57397222-chr12:57502661..57504882,2	MCF-7	breast:
8	chr12:57393282..57404587-chr12:57480276..57487045,17	MCF-7	breast:
9	chr12:57386989..57389481-chr12:57393031..57396730,3	K562	blood:
10	chr12:57394931..57395820-chr12:57506205..57506723,2	K562	blood:
11	chr12:57117267..57120560-chr12:57392029..57397065,4	K562	blood:
12	chr12:57393997..57397954-chr12:57398018..57401586,6	K562	blood:
13	chr12:57391978..57396253-chr12:57504502..57506587,3	MCF-7	breast:
14	chr12:57150977..57151614-chr12:57395177..57395873,2	K562	blood:
15	chr12:57381112..57381620-chr12:57394915..57395894,2	MCF-7	breast:
16	chr12:57233578..57234246-chr12:57395048..57395757,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000258442	Chromatin interaction
ENSG00000166881	Chromatin interaction
ENSG00000166860	Chromatin interaction
ENSG00000196531	Chromatin interaction
ENSG00000166888	Chromatin interaction
ENSG00000268162	Chromatin interaction
ENSG00000166856	Chromatin interaction
ENSG00000166886	Chromatin interaction

Extended variants
information (count: 113 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:109)

rs_ID	r²[population]
rs10400412	0.99[ASN][1000 genomes]
rs10400555	0.99[ASN][1000 genomes]
rs1044939	0.91[ASN][1000 genomes]
rs10506347	0.82[EUR][1000 genomes]
rs10506350	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10506351	0.91[ASN][1000 genomes]
rs1072670	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11832487	0.93[ASN][1000 genomes]
rs11834851	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11834856	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11836517	0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12099695	0.97[ASN][1000 genomes]
rs12810024	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12810837	0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12812499	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12815538	0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12818342	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12824682	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12827039	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12827286	0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1552245	0.94[ASN][1000 genomes]
rs17119301	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17119327	0.99[ASN][1000 genomes]
rs17119330	0.99[ASN][1000 genomes]
rs17119344	0.94[ASN][1000 genomes]
rs17119352	0.94[ASN][1000 genomes]
rs17119386	0.95[ASN][1000 genomes]
rs17119388	0.95[ASN][1000 genomes]
rs17119390	0.94[ASN][1000 genomes]
rs17119407	0.89[ASN][1000 genomes]
rs17119416	0.86[ASN][1000 genomes]
rs17119418	0.83[ASN][1000 genomes]
rs1843311	0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1843312	0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1843313	0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2167306	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2270736	0.94[ASN][1000 genomes]
rs2270737	0.94[ASN][1000 genomes]
rs2270739	0.82[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs2279373	0.97[ASN][1000 genomes]
rs2279743	0.96[ASN][1000 genomes]
rs2291855	0.99[ASN][1000 genomes]
rs2371717	1.00[ASN][1000 genomes]
rs28589663	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2888139	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34186462	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34253098	0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34359134	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34762603	0.86[ASN][1000 genomes]
rs34969650	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35034299	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35243318	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35493121	0.97[ASN][1000 genomes]
rs3782329	0.95[ASN][1000 genomes]
rs3782330	0.95[ASN][1000 genomes]
rs3803018	0.97[ASN][1000 genomes]
rs3894415	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4016338	1.00[ASN][1000 genomes]
rs4039	0.91[ASN][1000 genomes]
rs4143085	0.95[ASN][1000 genomes]
rs56128678	0.94[ASN][1000 genomes]
rs56270558	0.94[ASN][1000 genomes]
rs56354404	0.94[ASN][1000 genomes]
rs57056392	0.95[ASN][1000 genomes]
rs57129030	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs57351760	0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs57558853	0.99[ASN][1000 genomes]
rs58298943	0.96[ASN][1000 genomes]
rs58389529	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs60258120	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs60273384	0.97[ASN][1000 genomes]
rs60380217	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61504157	0.95[ASN][1000 genomes]
rs67476535	0.97[ASN][1000 genomes]
rs67771054	0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs67844278	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs68126184	0.96[ASN][1000 genomes]
rs697222	0.85[ASN][1000 genomes]
rs7135297	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7136770	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs71461303	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72482268	0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7298475	0.86[ASN][1000 genomes]
rs73114426	0.99[ASN][1000 genomes]
rs73114428	0.99[ASN][1000 genomes]
rs73114434	0.99[ASN][1000 genomes]
rs73114436	0.99[ASN][1000 genomes]
rs73114437	0.96[ASN][1000 genomes]
rs73114446	0.94[ASN][1000 genomes]
rs73114452	0.94[ASN][1000 genomes]
rs73114457	0.94[ASN][1000 genomes]
rs73114459	0.94[ASN][1000 genomes]
rs73114467	0.94[ASN][1000 genomes]
rs73114468	0.94[ASN][1000 genomes]
rs73114472	0.91[ASN][1000 genomes]
rs73116494	0.86[ASN][1000 genomes]
rs73116501	0.86[ASN][1000 genomes]
rs73118413	0.83[ASN][1000 genomes]
rs73131120	0.96[ASN][1000 genomes]
rs733629	0.99[ASN][1000 genomes]
rs746049	0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7487948	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs755221	0.94[ASN][1000 genomes]
rs7956166	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7961920	0.95[ASN][1000 genomes]
rs7962771	0.86[ASN][1000 genomes]
rs7969312	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7972615	1.00[ASN][1000 genomes]
rs901068	0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1040850	chr12:57055011-57679209	Strong transcription Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	181 gene(s)	inside rSNPs	diseases
2	nsv428590	chr12:57329214-57527358	Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Weak transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
3	nsv832428	chr12:57340609-57535694	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
4	nsv559022	chr12:57394123-57410389	Strong transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:57381400-57396400	Weak transcription	HMEC	breast
2	chr12:57381800-57396400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr12:57381800-57397000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
4	chr12:57383200-57398800	Weak transcription	Fetal Heart	heart
5	chr12:57385400-57396000	Weak transcription	Primary neutrophils fromperipheralblood	blood
6	chr12:57385600-57396200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr12:57389000-57398200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr12:57389000-57398600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr12:57389000-57398600	Strong transcription	Thymus	Thymus
10	chr12:57389200-57398600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr12:57389200-57398600	Strong transcription	Primary T cells from cord blood	blood
12	chr12:57389600-57396000	Weak transcription	Brain Angular Gyrus	brain
13	chr12:57389800-57396000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr12:57390800-57398400	Strong transcription	Dnd41	blood
15	chr12:57391000-57396400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr12:57391000-57398600	Strong transcription	Brain Substantia Nigra	brain
17	chr12:57391800-57395800	Weak transcription	Right Ventricle	heart
18	chr12:57391800-57396000	Genic enhancers	Primary T helper cells PMA-I stimulated	--
19	chr12:57391800-57398600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr12:57391800-57398600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr12:57392000-57398600	Strong transcription	HUES48 Cell Line	embryonic stem cell
22	chr12:57392000-57398600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
23	chr12:57392600-57399000	Weak transcription	Small Intestine	intestine
24	chr12:57393000-57398600	Strong transcription	H1 Cell Line	embryonic stem cell
25	chr12:57393000-57398600	Strong transcription	Monocytes-CD14+_RO01746	blood
26	chr12:57393000-57398800	Strong transcription	HUES6 Cell Line	embryonic stem cell
27	chr12:57393200-57398800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
28	chr12:57393400-57396000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr12:57393400-57398600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr12:57393400-57398800	Strong transcription	HUES64 Cell Line	embryonic stem cell
31	chr12:57393600-57396200	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr12:57393600-57398600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
33	chr12:57393600-57398800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr12:57393800-57396200	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr12:57393800-57398600	Strong transcription	Primary monocytes fromperipheralblood	blood
36	chr12:57394000-57396200	Genic enhancers	K562	blood
37	chr12:57394000-57397800	Strong transcription	ES-I3 Cell Line	embryonic stem cell
38	chr12:57394000-57398400	Strong transcription	Primary B cells from cord blood	blood
39	chr12:57394000-57398600	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr12:57394000-57398600	Strong transcription	NH-A	brain
41	chr12:57394200-57396400	Genic enhancers	Primary T helper cells fromperipheralblood	blood
42	chr12:57394200-57398400	Strong transcription	Fetal Kidney	kidney
43	chr12:57394200-57398600	Genic enhancers	Brain Germinal Matrix	brain
44	chr12:57394400-57396200	Genic enhancers	Fetal Brain Female	brain
45	chr12:57394400-57396600	Strong transcription	Hela-S3	cervix
46	chr12:57394400-57398400	Strong transcription	HSMM	muscle
47	chr12:57394400-57398600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr12:57394600-57396000	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
49	chr12:57394600-57398600	Genic enhancers	Spleen	Spleen
50	chr12:57394800-57396000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood

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