Variant report

Variant	rs12728678
Chromosome Location	chr1:154764715-154764716
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:154762462..154764736-chr1:154782523..154784216,2	MCF-7	breast:
2	chr1:154764144..154765879-chr1:154767700..154769213,2	MCF-7	breast:

Extended variants
information (count: 14 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs12135902	1.00[CHB][hapmap];0.90[JPT][hapmap];0.91[ASN][1000 genomes]
rs12726787	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs12744544	0.89[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.92[YRI][hapmap];0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs35657705	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs4845672	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs6691316	0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs883319	0.88[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[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	nsv948413	chr1:153974621-154797272	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	132 gene(s)	inside rSNPs	diseases
2	nsv532579	chr1:154548165-155262692	Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Weak transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	575 gene(s)	inside rSNPs	diseases
3	nsv427797	chr1:154559115-154933717	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
4	nsv470740	chr1:154568683-154796895	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
5	nsv464050	chr1:154568683-154801247	Weak transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
6	nsv547958	chr1:154568683-154801247	Enhancers Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
7	nsv872452	chr1:154750989-154769561	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:154756000-154767200	Enhancers	Fetal Thymus	thymus
2	chr1:154760600-154768200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr1:154762400-154766000	Enhancers	Thymus	Thymus
4	chr1:154762600-154765400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
5	chr1:154762600-154766000	Enhancers	Primary T cells fromperipheralblood	blood
6	chr1:154762800-154765600	Enhancers	Primary T helper cells PMA-I stimulated	--
7	chr1:154762800-154765800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr1:154763000-154765600	Enhancers	Primary hematopoietic stem cells	blood
9	chr1:154763000-154765600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
10	chr1:154763000-154765600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
11	chr1:154763000-154765600	Enhancers	Primary T killer memory cells from peripheral blood	blood
12	chr1:154763200-154765200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr1:154763200-154765800	Enhancers	Primary hematopoietic stem cells short term culture	blood
14	chr1:154763400-154766000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
15	chr1:154763600-154764800	Enhancers	Colon Smooth Muscle	Colon
16	chr1:154763800-154764800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
17	chr1:154763800-154764800	Enhancers	Fetal Muscle Leg	muscle
18	chr1:154763800-154764800	Enhancers	Psoas Muscle	Psoas
19	chr1:154763800-154764800	Enhancers	Skeletal Muscle Male	skeletal muscle
20	chr1:154763800-154764800	Enhancers	NHEK	skin
21	chr1:154763800-154765000	Enhancers	Brain Hippocampus Middle	brain
22	chr1:154763800-154765600	Flanking Active TSS	GM12878-XiMat	blood
23	chr1:154763800-154765800	Enhancers	Brain Anterior Caudate	brain
24	chr1:154763800-154766600	Enhancers	Cortex derived primary cultured neurospheres	brain
25	chr1:154764000-154764800	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
26	chr1:154764000-154764800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr1:154764000-154764800	Enhancers	Brain Inferior Temporal Lobe	brain
28	chr1:154764000-154764800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
29	chr1:154764000-154764800	Enhancers	Fetal Stomach	stomach
30	chr1:154764000-154764800	Enhancers	Rectal Smooth Muscle	rectum
31	chr1:154764000-154764800	Enhancers	Stomach Smooth Muscle	stomach
32	chr1:154764000-154765000	Enhancers	Brain Substantia Nigra	brain
33	chr1:154764000-154765200	Bivalent Enhancer	Dnd41	blood
34	chr1:154764200-154764800	Enhancers	Duodenum Mucosa	Duodenum
35	chr1:154764200-154764800	Enhancers	Fetal Brain Male	brain
36	chr1:154764400-154764800	Bivalent Enhancer	Primary mononuclear cells fromperipheralblood	Blood
37	chr1:154764400-154764800	Enhancers	HSMM	muscle
38	chr1:154764400-154764800	Bivalent Enhancer	HUVEC	blood vessel
39	chr1:154764400-154765000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
40	chr1:154764400-154765600	Enhancers	Primary T cells from cord blood	blood
41	chr1:154764400-154766400	Enhancers	Fetal Brain Female	brain
42	chr1:154764600-154764800	Enhancers	Lung	lung
43	chr1:154764600-154765200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
44	chr1:154764600-154765400	Enhancers	Skeletal Muscle Female	skeletal muscle
45	chr1:154764600-154765600	Enhancers	Primary T helper cells fromperipheralblood	blood
46	chr1:154764600-154765800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr1:154764600-154768800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr1:154764600-154770000	Weak transcription	Brain Angular Gyrus	brain
49	chr1:154764600-154773800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr1:154764600-154778400	Weak transcription	Right Atrium	heart

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