Variant report

Variant	rs12564733
Chromosome Location	chr1:9779288-9779289
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:9746141..9751802-chr1:9775034..9783332,13	K562	blood:
2	chr1:9776353..9779413-chr1:9969324..9972333,3	K562	blood:
3	chr1:9778823..9786788-chr1:9787182..9791476,8	K562	blood:
4	chr1:9778426..9780737-chr1:9796414..9798720,2	K562	blood:

Variant related genes	Relation type
ENSG00000171608	Chromatin interaction
ENSG00000231789	Chromatin interaction
ENSG00000178585	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs10864435	0.88[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs11121484	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1141402	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs12025864	0.82[AMR][1000 genomes]
rs12034313	0.82[AMR][1000 genomes]
rs12037599	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs12042293	0.82[AMR][1000 genomes]
rs72633866	0.85[ASN][1000 genomes]
rs7550295	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3385337	chr1:9105242-10082223	Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	549 gene(s)	inside rSNPs	diseases
2	nsv871610	chr1:9655795-10008221	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	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
4	nsv832203	chr1:9726632-9860209	Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:9750600-9813000	Weak transcription	Right Atrium	heart
2	chr1:9751000-9779800	Weak transcription	Brain Cingulate Gyrus	brain
3	chr1:9761000-9781600	Weak transcription	HSMMtube	muscle
4	chr1:9763200-9782400	Weak transcription	Brain Hippocampus Middle	brain
5	chr1:9768600-9787400	Weak transcription	Left Ventricle	heart
6	chr1:9769200-9783600	Weak transcription	Brain Angular Gyrus	brain
7	chr1:9770800-9782600	Weak transcription	Brain Substantia Nigra	brain
8	chr1:9771600-9782600	Weak transcription	Brain Anterior Caudate	brain
9	chr1:9772600-9788600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr1:9774600-9783400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr1:9774800-9782600	Strong transcription	Brain Germinal Matrix	brain
12	chr1:9775200-9779400	Transcr. at gene 5' and 3'	Primary T helper naive cells fromperipheralblood	blood
13	chr1:9775400-9782000	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr1:9775600-9783400	Strong transcription	Fetal Brain Female	brain
15	chr1:9776000-9779400	Genic enhancers	Primary monocytes fromperipheralblood	blood
16	chr1:9776000-9779600	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr1:9776200-9780000	Genic enhancers	Monocytes-CD14+_RO01746	blood
18	chr1:9776400-9780000	Enhancers	Placenta	Placenta
19	chr1:9776600-9779400	Enhancers	HUES6 Cell Line	embryonic stem cell
20	chr1:9776600-9779800	Flanking Active TSS	K562	blood
21	chr1:9776800-9781800	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr1:9777200-9779800	Weak transcription	Aorta	Aorta
23	chr1:9777200-9780200	Weak transcription	Brain Inferior Temporal Lobe	brain
24	chr1:9777200-9781000	Enhancers	HMEC	breast
25	chr1:9777600-9780200	Genic enhancers	Spleen	Spleen
26	chr1:9777600-9782000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr1:9777600-9782000	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr1:9777800-9779600	Genic enhancers	Esophagus	oesophagus
29	chr1:9777800-9780200	Weak transcription	Duodenum Smooth Muscle	Duodenum
30	chr1:9777800-9780200	Weak transcription	Ovary	ovary
31	chr1:9777800-9780600	Enhancers	A549	lung
32	chr1:9777800-9781200	Weak transcription	Gastric	stomach
33	chr1:9777800-9790200	Strong transcription	Primary neutrophils fromperipheralblood	blood
34	chr1:9777800-9790600	Weak transcription	Pancreatic Islets	Pancreatic Islet
35	chr1:9778000-9779400	Enhancers	Skeletal Muscle Male	skeletal muscle
36	chr1:9778000-9779800	Weak transcription	Right Ventricle	heart
37	chr1:9778000-9781200	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr1:9778000-9782200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr1:9778200-9780000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
40	chr1:9778200-9780800	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
41	chr1:9778200-9782200	Genic enhancers	Primary B cells from peripheral blood	blood
42	chr1:9778200-9782800	Weak transcription	Liver	Liver
43	chr1:9778200-9783400	Strong transcription	iPS-15b Cell Line	embryonic stem cell
44	chr1:9778200-9783400	Weak transcription	Fetal Lung	lung
45	chr1:9778400-9779400	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr1:9778400-9780200	Genic enhancers	Thymus	Thymus
47	chr1:9778400-9781000	Weak transcription	Fetal Muscle Leg	muscle
48	chr1:9778400-9781200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
49	chr1:9778400-9781400	Weak transcription	HUES48 Cell Line	embryonic stem cell
50	chr1:9778400-9781600	Weak transcription	H9 Cell Line	embryonic stem cell

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