Variant report

Variant	rs12499251
Chromosome Location	chr4:151178365-151178366
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	chr4:151175795..151178374-chr4:151178941..151181154,2	MCF-7	breast:

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10007294	0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10021938	0.87[EUR][1000 genomes]
rs10022107	0.87[EUR][1000 genomes]
rs12499400	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12503255	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12512965	0.94[AFR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13434795	0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs17632340	0.87[EUR][1000 genomes]
rs28373995	0.87[EUR][1000 genomes]
rs28456277	0.87[EUR][1000 genomes]
rs28573941	0.87[EUR][1000 genomes]
rs28587623	0.87[EUR][1000 genomes]
rs28623363	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28680477	0.94[AFR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs57925391	0.87[EUR][1000 genomes]
rs6848342	0.87[EUR][1000 genomes]
rs72953804	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs72955819	0.87[EUR][1000 genomes]
rs9307872	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9307873	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9307875	0.87[EUR][1000 genomes]
rs9992387	0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1026797	chr4:150246932-151217137	Bivalent Enhancer Enhancers Strong transcription Flanking Active TSS Active TSS Weak transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	nsv932022	chr4:150831733-151419552	Enhancers Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv1032689	chr4:150971003-151316856	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv537300	chr4:150971003-151316856	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv880256	chr4:151126725-151751369	Enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv1022132	chr4:151162048-151183859	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
7	nsv880257	chr4:151170387-151231371	Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
8	nsv880258	chr4:151171082-151190804	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:92 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:151139600-151181000	Weak transcription	Brain Angular Gyrus	brain
2	chr4:151158000-151181000	Weak transcription	Fetal Heart	heart
3	chr4:151160000-151185400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr4:151166400-151181000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
5	chr4:151166400-151199000	Weak transcription	Gastric	stomach
6	chr4:151166600-151181000	Weak transcription	Fetal Kidney	kidney
7	chr4:151169800-151181000	Weak transcription	Brain Cingulate Gyrus	brain
8	chr4:151170000-151187000	Weak transcription	NH-A	brain
9	chr4:151170000-151199000	Weak transcription	Skeletal Muscle Male	skeletal muscle
10	chr4:151171200-151186800	Weak transcription	Pancreas	Pancrea
11	chr4:151172000-151181000	Weak transcription	Spleen	Spleen
12	chr4:151172000-151185400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr4:151172800-151179400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr4:151172800-151185400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr4:151172800-151188200	Strong transcription	Cortex derived primary cultured neurospheres	brain
16	chr4:151172800-151201600	Weak transcription	GM12878-XiMat	blood
17	chr4:151173000-151179600	Strong transcription	Brain Germinal Matrix	brain
18	chr4:151173000-151180000	Strong transcription	HSMMtube	muscle
19	chr4:151173000-151182200	Strong transcription	Fetal Brain Female	brain
20	chr4:151173000-151184600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr4:151173200-151178600	Strong transcription	Osteobl	bone
22	chr4:151173200-151192000	Weak transcription	Fetal Brain Male	brain
23	chr4:151173400-151178400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
24	chr4:151173400-151183800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr4:151173400-151184200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr4:151173400-151201400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr4:151173600-151180800	Weak transcription	Brain Hippocampus Middle	brain
28	chr4:151173800-151179200	Strong transcription	Fetal Muscle Leg	muscle
29	chr4:151173800-151186800	Weak transcription	Aorta	Aorta
30	chr4:151174200-151179400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr4:151175000-151185400	Weak transcription	NHLF	lung
32	chr4:151175400-151188000	Weak transcription	Primary hematopoietic stem cells	blood
33	chr4:151175800-151178600	Weak transcription	HSMM	muscle
34	chr4:151175800-151180400	Weak transcription	Brain Inferior Temporal Lobe	brain
35	chr4:151175800-151186800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
36	chr4:151175800-151186800	Weak transcription	Ovary	ovary
37	chr4:151176000-151181200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr4:151176000-151182800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr4:151176200-151181000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
40	chr4:151176400-151178400	Genic enhancers	Fetal Stomach	stomach
41	chr4:151176400-151178600	Enhancers	Sigmoid Colon	Sigmoid Colon
42	chr4:151176400-151202800	Weak transcription	Psoas Muscle	Psoas
43	chr4:151176600-151178400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr4:151176600-151180000	Enhancers	Breast Myoepithelial Primary Cells	Breast
45	chr4:151176600-151181000	Genic enhancers	Fetal Intestine Small	intestine
46	chr4:151176600-151185400	Weak transcription	Adipose Nuclei	Adipose
47	chr4:151176800-151178400	Strong transcription	Right Ventricle	heart
48	chr4:151177000-151178400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr4:151177000-151178600	Enhancers	HUES6 Cell Line	embryonic stem cell
50	chr4:151177000-151180000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links