Variant report

Variant	rs2458404
Chromosome Location	chr12:122155986-122155987
allele	C/G
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:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:122144623..122148014-chr12:122154600..122158255,3	MCF-7	breast:
2	chr12:122154851..122156894-chr12:122210970..122213688,2	MCF-7	breast:
3	chr12:122155312..122157141-chr12:122174374..122176796,2	K562	blood:
4	chr12:122151917..122156679-chr12:122158990..122161990,5	MCF-7	breast:
5	chr12:122154279..122156536-chr12:122192092..122194688,2	MCF-7	breast:
6	chr12:122154946..122156536-chr12:122242175..122243926,2	MCF-7	breast:
7	chr12:122149668..122153356-chr12:122153508..122157452,6	K562	blood:
8	chr12:122155468..122157385-chr12:122229687..122232210,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000188735	Chromatin interaction
ENSG00000139718	Chromatin interaction
ENSG00000139725	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs11043184	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12320939	0.86[GIH][hapmap]
rs2669166	0.91[GIH][hapmap]
rs2669172	0.96[CEU][hapmap];0.91[CHB][hapmap];0.89[CHD][hapmap];0.86[JPT][hapmap];0.96[MEX][hapmap];0.94[TSI][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2720036	0.96[CEU][hapmap];0.87[CHB][hapmap];0.86[JPT][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2942368	0.89[GIH][hapmap]
rs2942375	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2942376	0.95[CEU][hapmap];0.86[CHB][hapmap];0.83[EUR][1000 genomes]
rs2942377	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2942378	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2942379	0.91[GIH][hapmap]
rs884885	0.96[CEU][hapmap];0.91[CHB][hapmap];0.86[JPT][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs925530	0.96[CEU][hapmap];0.91[CHB][hapmap];0.89[CHD][hapmap];0.86[JPT][hapmap];0.96[MEX][hapmap];0.94[TSI][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9804982	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[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	nsv529868	chr12:121956483-122944265	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	173 gene(s)	inside rSNPs	diseases
2	nsv1040169	chr12:122096825-122209555	Flanking Active TSS Weak transcription Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:90 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:122151600-122160800	Weak transcription	Aorta	Aorta
2	chr12:122151600-122186200	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr12:122151800-122158000	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr12:122151800-122159200	Weak transcription	Esophagus	oesophagus
5	chr12:122151800-122160600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr12:122152000-122156600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr12:122152000-122161200	Weak transcription	Gastric	stomach
8	chr12:122152000-122162600	Weak transcription	Primary T helper cells fromperipheralblood	blood
9	chr12:122152000-122164000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr12:122152000-122164000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr12:122152000-122164600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
12	chr12:122152000-122166400	Weak transcription	Rectal Mucosa Donor 29	rectum
13	chr12:122152000-122167400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
14	chr12:122152000-122182200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr12:122152000-122188000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr12:122152200-122157800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr12:122152200-122157800	Weak transcription	HMEC	breast
18	chr12:122152200-122160600	Weak transcription	Left Ventricle	heart
19	chr12:122152200-122161200	Weak transcription	Right Atrium	heart
20	chr12:122152200-122162800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
21	chr12:122152200-122162800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
22	chr12:122152200-122162800	Weak transcription	Liver	Liver
23	chr12:122152200-122165000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr12:122152200-122166600	Weak transcription	Ovary	ovary
25	chr12:122152200-122181600	Weak transcription	Cortex derived primary cultured neurospheres	brain
26	chr12:122152200-122181800	Weak transcription	Right Ventricle	heart
27	chr12:122152200-122186400	Weak transcription	Duodenum Mucosa	Duodenum
28	chr12:122152200-122188000	Weak transcription	Brain Germinal Matrix	brain
29	chr12:122152200-122188000	Weak transcription	Dnd41	blood
30	chr12:122152200-122191600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
31	chr12:122152200-122191600	Weak transcription	Rectal Smooth Muscle	rectum
32	chr12:122152200-122200200	Weak transcription	Duodenum Smooth Muscle	Duodenum
33	chr12:122152400-122161800	Weak transcription	Fetal Brain Male	brain
34	chr12:122152400-122171600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr12:122152400-122188000	Weak transcription	Stomach Smooth Muscle	stomach
36	chr12:122152800-122169200	Weak transcription	Fetal Brain Female	brain
37	chr12:122152800-122186200	Weak transcription	Pancreas	Pancrea
38	chr12:122153200-122159600	Strong transcription	Fetal Stomach	stomach
39	chr12:122153400-122158200	Enhancers	Skeletal Muscle Female	skeletal muscle
40	chr12:122153600-122166400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr12:122153800-122156600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
42	chr12:122154000-122162800	Weak transcription	Brain Anterior Caudate	brain
43	chr12:122154000-122182200	Weak transcription	Primary T cells from cord blood	blood
44	chr12:122154200-122165200	Weak transcription	Fetal Intestine Large	intestine
45	chr12:122154200-122200400	Weak transcription	Psoas Muscle	Psoas
46	chr12:122154800-122158600	Enhancers	Placenta	Placenta
47	chr12:122155000-122165200	Weak transcription	HepG2	liver
48	chr12:122155200-122156000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr12:122155200-122156400	Weak transcription	Fetal Thymus	thymus
50	chr12:122155200-122156800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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