Variant report

Variant	rs12406448
Chromosome Location	chr1:10106775-10106776
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:10001503..10004975-chr1:10105430..10108846,3	MCF-7	breast:
2	chr1:10106569..10108860-chr1:10117865..10121125,3	K562	blood:
3	chr1:10106280..10108164-chr1:10128537..10130148,2	K562	blood:
4	chr1:10101497..10103283-chr1:10104322..10107191,2	K562	blood:
5	chr1:10104211..10106912-chr1:10107965..10110739,3	K562	blood:
6	chr1:10091336..10093610-chr1:10105600..10107444,2	K562	blood:

Variant related genes	Relation type
ENSG00000228150	Chromatin interaction
ENSG00000130939	Chromatin interaction
ENSG00000173614	Chromatin interaction
ENSG00000162441	Chromatin interaction
ENSG00000233623	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs11578833	1.00[CEU][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes]
rs11589489	1.00[CEU][hapmap];1.00[AFR][1000 genomes]
rs13374181	1.00[AFR][1000 genomes]
rs6696978	0.86[JPT][hapmap]
rs72638953	0.88[AMR][1000 genomes]
rs72638984	1.00[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3417409	chr1:9683992-10241703	Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	nsv1012469	chr1:9925714-10147796	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	nsv1012301	chr1:9963962-10118393	Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
4	nsv534853	chr1:9963962-10118393	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
5	nsv1001742	chr1:9971776-10116767	Flanking Active TSS Enhancers Active TSS Strong transcription Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
6	nsv527217	chr1:10093457-10257167	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:10094800-10119400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr1:10095000-10108000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
3	chr1:10095000-10111400	Weak transcription	GM12878-XiMat	blood
4	chr1:10095000-10115000	Weak transcription	A549	lung
5	chr1:10095000-10115400	Weak transcription	Muscle Satellite Cultured Cells	--
6	chr1:10095000-10116000	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr1:10095000-10116200	Weak transcription	HSMM	muscle
8	chr1:10095000-10127800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr1:10095000-10147600	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr1:10095200-10134400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
11	chr1:10095400-10115600	Weak transcription	HUVEC	blood vessel
12	chr1:10098000-10109200	Weak transcription	Dnd41	blood
13	chr1:10098800-10116000	Weak transcription	Hela-S3	cervix
14	chr1:10098800-10131200	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr1:10101600-10107200	Strong transcription	Thymus	Thymus
16	chr1:10101800-10113400	Strong transcription	Monocytes-CD14+_RO01746	blood
17	chr1:10103000-10107600	Weak transcription	Fetal Thymus	thymus
18	chr1:10103000-10116200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr1:10103200-10108800	Weak transcription	Primary B cells from cord blood	blood
20	chr1:10104000-10109400	Weak transcription	Primary neutrophils fromperipheralblood	blood
21	chr1:10104400-10109000	Enhancers	Brain Cingulate Gyrus	brain
22	chr1:10104600-10107400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr1:10104600-10107400	Enhancers	Fetal Heart	heart
24	chr1:10104600-10107400	Enhancers	Pancreas	Pancrea
25	chr1:10104600-10107600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr1:10104600-10108200	Enhancers	Brain Angular Gyrus	brain
27	chr1:10104600-10108200	Enhancers	Ovary	ovary
28	chr1:10104600-10108800	Enhancers	Brain Substantia Nigra	brain
29	chr1:10104800-10107200	Enhancers	Gastric	stomach
30	chr1:10104800-10107400	Enhancers	Breast Myoepithelial Primary Cells	Breast
31	chr1:10105000-10107400	Enhancers	Liver	Liver
32	chr1:10105000-10107400	Enhancers	Psoas Muscle	Psoas
33	chr1:10105200-10106800	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr1:10105200-10107200	Enhancers	Fetal Lung	lung
35	chr1:10105200-10107200	Enhancers	Placenta	Placenta
36	chr1:10105200-10107200	Enhancers	Right Atrium	heart
37	chr1:10105200-10107400	Enhancers	iPS-18 Cell Line	embryonic stem cell
38	chr1:10105200-10107400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr1:10105200-10107400	Enhancers	Brain Inferior Temporal Lobe	brain
40	chr1:10105200-10107400	Enhancers	Right Ventricle	heart
41	chr1:10105200-10107600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
42	chr1:10105200-10109400	Enhancers	Left Ventricle	heart
43	chr1:10105200-10113200	Strong transcription	Primary T cells from cord blood	blood
44	chr1:10105400-10106800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr1:10105400-10107000	Enhancers	Lung	lung
46	chr1:10105400-10107200	Enhancers	HUES64 Cell Line	embryonic stem cell
47	chr1:10105400-10107200	Enhancers	Fetal Brain Female	brain
48	chr1:10105400-10107400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr1:10105400-10107600	Enhancers	Esophagus	oesophagus
50	chr1:10105400-10109000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood

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