Variant report

Variant	rs34587940
Chromosome Location	chr12:124391495-124391496
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:124389950..124393053-chr12:124455413..124457949,3	MCF-7	breast:
2	chr12:124295197..124298095-chr12:124388889..124391568,2	MCF-7	breast:
3	chr12:124389629..124391597-chr12:124394347..124396284,2	K562	blood:

Variant related genes	Relation type
ENSG00000179195	Chromatin interaction
ENSG00000119242	Chromatin interaction
ENSG00000178882	Chromatin interaction
ENSG00000270095	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10773046	0.86[ASN][1000 genomes]
rs10773047	0.84[ASN][1000 genomes]
rs10846570	0.85[ASN][1000 genomes]
rs10846571	0.85[ASN][1000 genomes]
rs10846572	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10846573	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10846574	0.82[ASN][1000 genomes]
rs10846575	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10846576	0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11057388	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11057389	0.87[ASN][1000 genomes]
rs11057390	0.86[ASN][1000 genomes]
rs11057391	0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12306328	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12307524	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12309481	0.97[ASN][1000 genomes]
rs1317386	0.82[ASN][1000 genomes]
rs2341569	0.93[ASN][1000 genomes]
rs28435362	0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28528904	0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28654550	0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4390427	0.84[ASN][1000 genomes]
rs57078519	0.97[ASN][1000 genomes]
rs57316347	0.97[ASN][1000 genomes]
rs58411567	0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61587964	0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6488910	0.97[ASN][1000 genomes]
rs7296123	0.87[ASN][1000 genomes]
rs7297429	0.81[ASN][1000 genomes]
rs7303634	0.86[ASN][1000 genomes]
rs7314278	0.87[ASN][1000 genomes]
rs7964324	0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7970597	0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7976319	0.97[ASN][1000 genomes]
rs7977078	0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7978781	0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv498024	chr12:123994372-124459856	Active TSS Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	esv1811815	chr12:124374716-124424636	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	esv1832870	chr12:124374716-124424636	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv522321	chr12:124383950-124424636	Enhancers Strong transcription Genic enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv560499	chr12:124389150-124396816	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:124384000-124408400	Weak transcription	Fetal Brain Female	brain
2	chr12:124386000-124395800	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr12:124386200-124392000	Weak transcription	NH-A	brain
4	chr12:124386200-124392200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr12:124386200-124394000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr12:124386800-124391800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr12:124387200-124392000	Weak transcription	Fetal Thymus	thymus
8	chr12:124388400-124391800	Weak transcription	Cortex derived primary cultured neurospheres	brain
9	chr12:124390000-124392200	Weak transcription	Brain Hippocampus Middle	brain
10	chr12:124390200-124391600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr12:124390200-124391600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr12:124390200-124391800	Weak transcription	Fetal Kidney	kidney
13	chr12:124390200-124391800	Weak transcription	HMEC	breast
14	chr12:124390200-124397600	Weak transcription	Primary neutrophils fromperipheralblood	blood
15	chr12:124390400-124391600	Weak transcription	NHDF-Ad	bronchial
16	chr12:124390400-124392000	Weak transcription	Brain Cingulate Gyrus	brain
17	chr12:124390400-124392000	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr12:124390400-124392000	Weak transcription	Fetal Intestine Small	intestine
19	chr12:124390400-124392400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr12:124390600-124391800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr12:124390800-124392200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr12:124390800-124394400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr12:124391400-124392200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
24	chr12:124391400-124392600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr12:124391400-124392800	Enhancers	Fetal Lung	lung
26	chr12:124391400-124393000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr12:124391400-124393000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr12:124391400-124393600	Enhancers	Breast Myoepithelial Primary Cells	Breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links