Variant report

Variant	rs12409024
Chromosome Location	chr1:151495330-151495331
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:151491040..151494428-chr1:151495030..151499382,4	MCF-7	breast:
2	chr1:151494134..151498303-chr1:151504253..151506959,4	MCF-7	breast:
3	chr1:151493742..151497338-chr1:151500122..151502548,3	MCF-7	breast:
4	chr1:151488223..151491246-chr1:151492945..151496772,3	K562	blood:
5	chr1:151494437..151499363-chr1:151510633..151514422,7	MCF-7	breast:
6	chr1:151491469..151494027-chr1:151494833..151497937,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000232536	Chromatin interaction
ENSG00000252840	Chromatin interaction
ENSG00000143375	Chromatin interaction
ENSG00000143367	Chromatin interaction

Extended variants
information (count: 5 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs4970916	0.90[EUR][1000 genomes]
rs72633636	0.81[EUR][1000 genomes]
rs7547590	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916272	chr1:150961809-151557253	Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	219 gene(s)	inside rSNPs	diseases
2	nsv997511	chr1:151491765-151595902	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	90 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:151484600-151512000	Weak transcription	Right Atrium	heart
2	chr1:151485200-151511800	Weak transcription	Fetal Brain Female	brain
3	chr1:151485800-151511800	Weak transcription	Brain Germinal Matrix	brain
4	chr1:151485800-151512200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr1:151486000-151501800	Weak transcription	Rectal Smooth Muscle	rectum
6	chr1:151486600-151511800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr1:151486800-151512200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr1:151487000-151501800	Weak transcription	Esophagus	oesophagus
9	chr1:151487000-151511800	Weak transcription	Small Intestine	intestine
10	chr1:151487200-151502400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr1:151487400-151501000	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr1:151489000-151497200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr1:151489000-151499400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr1:151489200-151507000	Weak transcription	NHEK	skin
15	chr1:151489200-151507400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr1:151490000-151496200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr1:151491000-151500000	Strong transcription	Rectal Mucosa Donor 31	rectum
18	chr1:151491000-151505200	Strong transcription	Duodenum Mucosa	Duodenum
19	chr1:151491600-151496600	Weak transcription	Lung	lung
20	chr1:151491600-151509000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr1:151492000-151507400	Weak transcription	Stomach Mucosa	stomach
22	chr1:151492200-151496000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr1:151492600-151495800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr1:151492600-151496600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr1:151492800-151496600	Weak transcription	Brain Substantia Nigra	brain
26	chr1:151493000-151496600	Weak transcription	Brain Angular Gyrus	brain
27	chr1:151493000-151496800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr1:151493200-151495800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr1:151493200-151496000	Weak transcription	Cortex derived primary cultured neurospheres	brain
30	chr1:151493200-151496800	Weak transcription	GM12878-XiMat	blood
31	chr1:151493200-151497600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
32	chr1:151493200-151501000	Weak transcription	HMEC	breast
33	chr1:151493200-151507600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr1:151493400-151495600	Weak transcription	Brain Cingulate Gyrus	brain
35	chr1:151493400-151495800	Weak transcription	H9 Cell Line	embryonic stem cell
36	chr1:151493400-151495800	Weak transcription	Gastric	stomach
37	chr1:151493400-151495800	Weak transcription	Placenta Amnion	Placenta Amnion
38	chr1:151493400-151495800	Weak transcription	Sigmoid Colon	Sigmoid Colon
39	chr1:151493400-151496000	Weak transcription	Brain Inferior Temporal Lobe	brain
40	chr1:151493400-151496000	Strong transcription	Fetal Intestine Small	intestine
41	chr1:151493400-151496400	Weak transcription	Pancreas	Pancrea
42	chr1:151493400-151496800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
43	chr1:151493400-151501200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr1:151493400-151501200	Weak transcription	Colonic Mucosa	Colon
45	chr1:151493400-151501800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
46	chr1:151493400-151511800	Weak transcription	Brain Anterior Caudate	brain
47	chr1:151493400-151511800	Weak transcription	Ovary	ovary
48	chr1:151493400-151512200	Weak transcription	Fetal Kidney	kidney
49	chr1:151493600-151495600	Weak transcription	HUES6 Cell Line	embryonic stem cell
50	chr1:151493600-151511200	Strong transcription	Fetal Intestine Large	intestine

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