Variant report

Variant	rs6734923
Chromosome Location	chr2:169727730-169727731
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 23 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs1467278	0.87[EUR][1000 genomes]
rs2632380	0.96[ASN][1000 genomes]
rs2632382	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2685799	0.88[ASN][1000 genomes]
rs480731	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs488621	0.96[ASN][1000 genomes]
rs493816	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs497808	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs506362	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs527393	0.96[ASN][1000 genomes]
rs540652	0.96[ASN][1000 genomes]
rs543727	0.87[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs554494	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs560952	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs569997	0.96[ASN][1000 genomes]
rs576062	0.95[ASN][1000 genomes]
rs7582529	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs830193	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs844213	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9751269	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9753196	0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[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	nsv583599	chr2:169664227-169903096	Bivalent Enhancer Weak transcription Genic enhancers Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
2	nsv875381	chr2:169686559-169749841	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6734923	SPC25	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:169698600-169744600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr2:169702200-169733000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr2:169706600-169727800	Weak transcription	Primary monocytes fromperipheralblood	blood
4	chr2:169709800-169733400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr2:169712600-169727800	Weak transcription	Primary T cells from cord blood	blood
6	chr2:169713200-169728800	Weak transcription	Primary hematopoietic stem cells	blood
7	chr2:169713400-169731200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr2:169714000-169732800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr2:169715400-169731600	Weak transcription	Small Intestine	intestine
10	chr2:169715400-169746200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr2:169716000-169745800	Weak transcription	HSMM	muscle
12	chr2:169717000-169746400	Weak transcription	Primary B cells from cord blood	blood
13	chr2:169719800-169733600	Weak transcription	NHDF-Ad	bronchial
14	chr2:169721600-169727800	Weak transcription	Cortex derived primary cultured neurospheres	brain
15	chr2:169721800-169728000	Weak transcription	Primary neutrophils fromperipheralblood	blood
16	chr2:169722000-169727800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr2:169722000-169727800	Weak transcription	HUES48 Cell Line	embryonic stem cell
18	chr2:169722000-169727800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr2:169722000-169727800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr2:169722000-169727800	Weak transcription	Dnd41	blood
21	chr2:169722000-169728000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr2:169722000-169728000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
23	chr2:169722000-169728000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr2:169722000-169728000	Weak transcription	HepG2	liver
25	chr2:169722000-169728000	Weak transcription	K562	blood
26	chr2:169722000-169728000	Weak transcription	Monocytes-CD14+_RO01746	blood
27	chr2:169722000-169728200	Weak transcription	A549	lung
28	chr2:169722000-169728200	Weak transcription	HUVEC	blood vessel
29	chr2:169722000-169728400	Weak transcription	Thymus	Thymus
30	chr2:169722000-169729000	Weak transcription	HMEC	breast
31	chr2:169722000-169730600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr2:169722000-169730800	Weak transcription	Rectal Mucosa Donor 29	rectum
33	chr2:169722000-169730800	Weak transcription	Rectal Mucosa Donor 31	rectum
34	chr2:169722000-169732800	Weak transcription	Fetal Heart	heart
35	chr2:169722000-169736200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr2:169722000-169741200	Weak transcription	H1 Cell Line	embryonic stem cell
37	chr2:169722000-169741400	Weak transcription	Muscle Satellite Cultured Cells	--
38	chr2:169722000-169741400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr2:169722000-169741400	Weak transcription	NHEK	skin
40	chr2:169722000-169741800	Weak transcription	Fetal Lung	lung
41	chr2:169722000-169742800	Weak transcription	Fetal Muscle Trunk	muscle
42	chr2:169722000-169744000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr2:169722000-169745800	Weak transcription	Fetal Stomach	stomach
44	chr2:169722000-169745800	Weak transcription	GM12878-XiMat	blood
45	chr2:169722000-169746000	Weak transcription	H9 Cell Line	embryonic stem cell
46	chr2:169722000-169746000	Weak transcription	Fetal Intestine Large	intestine
47	chr2:169722000-169746000	Weak transcription	Fetal Intestine Small	intestine
48	chr2:169722000-169746000	Weak transcription	Fetal Muscle Leg	muscle
49	chr2:169722200-169727800	Weak transcription	Fetal Thymus	thymus
50	chr2:169722200-169728000	Weak transcription	HUES6 Cell Line	embryonic stem cell

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