Variant report

Variant	rs6452796
Chromosome Location	chr5:70780589-70780590
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:70761475..70763695-chr5:70779262..70782933,3	K562	blood:
2	chr5:70780373..70782850-chr5:70784196..70785827,2	K562	blood:
3	chr5:70779922..70782030-chr5:70836622..70838928,2	K562	blood:

Extended variants
information (count: 9 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs12514732	0.82[AMR][1000 genomes]
rs12516456	0.85[TSI][hapmap]
rs6453021	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7378819	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7711253	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7721025	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1034703	chr5:70391173-70995695	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	nsv882176	chr5:70738250-70860665	Genic enhancers Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	esv2754424	chr5:70749744-70885544	Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs6452796	CENPH	cis	parietal	SCAN
rs6452796	MCCC2	Cis_1M	lymphoblastoid	RTeQTL
rs6452796	FAM169A	cis	parietal	SCAN
rs6452796	SMN1	cis	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:70752600-70789200	Weak transcription	Small Intestine	intestine
2	chr5:70752600-70794800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr5:70753000-70781400	Weak transcription	Fetal Heart	heart
4	chr5:70754200-70815800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr5:70754400-70795800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr5:70754400-70807200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
7	chr5:70754400-70809800	Strong transcription	Fetal Intestine Large	intestine
8	chr5:70754400-70824200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr5:70754600-70820400	Strong transcription	Primary T helper cells fromperipheralblood	blood
10	chr5:70754600-70820400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr5:70759800-70833400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr5:70760200-70798400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr5:70761800-70786800	Weak transcription	Aorta	Aorta
14	chr5:70765400-70820400	Strong transcription	Primary monocytes fromperipheralblood	blood
15	chr5:70765400-70820400	Strong transcription	Primary B cells from peripheral blood	blood
16	chr5:70766000-70820400	Strong transcription	Monocytes-CD14+_RO01746	blood
17	chr5:70766200-70807000	Strong transcription	Fetal Muscle Trunk	muscle
18	chr5:70766800-70782000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
19	chr5:70767000-70781800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr5:70768000-70782000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
21	chr5:70770000-70783800	Strong transcription	Fetal Lung	lung
22	chr5:70770600-70783200	Weak transcription	Brain Cingulate Gyrus	brain
23	chr5:70771000-70789400	Strong transcription	Primary neutrophils fromperipheralblood	blood
24	chr5:70771000-70794600	Weak transcription	Colonic Mucosa	Colon
25	chr5:70771200-70792200	Weak transcription	Spleen	Spleen
26	chr5:70771400-70820400	Strong transcription	HUES64 Cell Line	embryonic stem cell
27	chr5:70771800-70799200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr5:70773200-70783000	Weak transcription	Cortex derived primary cultured neurospheres	brain
29	chr5:70773400-70783200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr5:70774000-70793600	Weak transcription	Lung	lung
31	chr5:70774400-70820400	Strong transcription	Fetal Thymus	thymus
32	chr5:70775600-70821000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
33	chr5:70776000-70806200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
34	chr5:70776400-70819200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr5:70776400-70820400	Strong transcription	HUES48 Cell Line	embryonic stem cell
36	chr5:70776400-70820400	Strong transcription	Primary T cells fromperipheralblood	blood
37	chr5:70776400-70820400	Strong transcription	Duodenum Mucosa	Duodenum
38	chr5:70776600-70820400	Strong transcription	HUES6 Cell Line	embryonic stem cell
39	chr5:70776800-70789000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr5:70776800-70795400	Strong transcription	GM12878-XiMat	blood
41	chr5:70776800-70820400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
42	chr5:70776800-70820400	Strong transcription	Dnd41	blood
43	chr5:70777000-70783200	Weak transcription	Esophagus	oesophagus
44	chr5:70777000-70785400	Weak transcription	Placenta Amnion	Placenta Amnion
45	chr5:70777200-70783400	Weak transcription	Pancreas	Pancrea
46	chr5:70777400-70781600	Weak transcription	Fetal Kidney	kidney
47	chr5:70777400-70783000	Weak transcription	Fetal Intestine Small	intestine
48	chr5:70777400-70783200	Weak transcription	Thymus	Thymus
49	chr5:70777400-70783400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr5:70777400-70791200	Strong transcription	Primary B cells from cord blood	blood

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