Variant report

Variant	rs6877561
Chromosome Location	chr5:59940502-59940503
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 47 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10939855	0.81[ASN][1000 genomes]
rs10939856	0.82[ASN][1000 genomes]
rs11739724	0.82[ASN][1000 genomes]
rs11948543	0.91[ASN][1000 genomes]
rs11951503	0.91[ASN][1000 genomes]
rs11951950	0.85[ASN][1000 genomes]
rs11952735	0.91[ASN][1000 genomes]
rs11956023	0.88[ASN][1000 genomes]
rs11959922	0.92[ASN][1000 genomes]
rs1379116	0.91[ASN][1000 genomes]
rs1379117	0.91[ASN][1000 genomes]
rs1562235	0.85[ASN][1000 genomes]
rs187481	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2061250	0.89[ASN][1000 genomes]
rs206789	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2198865	0.90[ASN][1000 genomes]
rs2409791	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs249070	0.84[ASN][1000 genomes]
rs2591636	0.89[ASN][1000 genomes]
rs286153	0.94[ASN][1000 genomes]
rs286155	0.94[ASN][1000 genomes]
rs286156	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs286158	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2898287	0.85[ASN][1000 genomes]
rs3857236	0.89[ASN][1000 genomes]
rs3958943	0.84[ASN][1000 genomes]
rs4326096	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4515250	0.89[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs4699959	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4700378	0.81[ASN][1000 genomes]
rs4700379	0.83[ASN][1000 genomes]
rs4700380	0.89[ASN][1000 genomes]
rs4700381	0.86[ASN][1000 genomes]
rs5012862	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs55720622	0.81[ASN][1000 genomes]
rs55768631	0.84[ASN][1000 genomes]
rs56137970	0.85[ASN][1000 genomes]
rs56166952	0.89[ASN][1000 genomes]
rs56191602	0.90[ASN][1000 genomes]
rs59155887	0.89[ASN][1000 genomes]
rs62372964	0.86[ASN][1000 genomes]
rs6449478	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6449480	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6896942	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7725028	0.87[AMR][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	nsv598288	chr5:59627555-60003460	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
2	nsv492277	chr5:59905195-60180834	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6877561	ELOVL7	Cis_1M	lymphoblastoid	RTeQTL
rs6877561	DEPDC1B	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:59920600-59947800	Weak transcription	HUVEC	blood vessel
2	chr5:59924400-59941800	Weak transcription	Fetal Brain Female	brain
3	chr5:59925000-59942800	Strong transcription	Dnd41	blood
4	chr5:59925200-59947200	Weak transcription	Pancreas	Pancrea
5	chr5:59926400-59967800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr5:59926600-59946200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr5:59927200-59944000	Weak transcription	Fetal Muscle Leg	muscle
8	chr5:59927400-59941200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr5:59928400-59942800	Weak transcription	Duodenum Mucosa	Duodenum
10	chr5:59929400-59942800	Weak transcription	Fetal Intestine Small	intestine
11	chr5:59929400-59944400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
12	chr5:59929400-59947400	Weak transcription	Muscle Satellite Cultured Cells	--
13	chr5:59929400-59954600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr5:59929600-59948000	Weak transcription	NHEK	skin
15	chr5:59930000-59943400	Strong transcription	Placenta	Placenta
16	chr5:59930200-59941200	Weak transcription	Fetal Lung	lung
17	chr5:59931200-59942600	Strong transcription	HUES48 Cell Line	embryonic stem cell
18	chr5:59931400-59941400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr5:59932000-59944200	Weak transcription	Primary hematopoietic stem cells	blood
20	chr5:59932400-59940600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
21	chr5:59932400-59941800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr5:59932800-59941200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
23	chr5:59933200-59942400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr5:59933400-59965200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr5:59933600-59940600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
26	chr5:59933600-59944000	Weak transcription	Fetal Stomach	stomach
27	chr5:59933600-59981000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr5:59933800-59942400	Strong transcription	HUES6 Cell Line	embryonic stem cell
29	chr5:59934000-59943000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr5:59934800-59947600	Weak transcription	HMEC	breast
31	chr5:59936000-59941400	Strong transcription	HepG2	liver
32	chr5:59936600-59961400	Weak transcription	Thymus	Thymus
33	chr5:59936800-59961800	Weak transcription	Fetal Thymus	thymus
34	chr5:59937000-59943000	Weak transcription	Sigmoid Colon	Sigmoid Colon
35	chr5:59937000-59945800	Weak transcription	GM12878-XiMat	blood
36	chr5:59937400-59941200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr5:59937400-59943400	Strong transcription	HUES64 Cell Line	embryonic stem cell
38	chr5:59937600-59940600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr5:59937600-59941000	Strong transcription	Primary monocytes fromperipheralblood	blood
40	chr5:59937800-59940600	Strong transcription	Fetal Intestine Large	intestine
41	chr5:59938000-59940600	Strong transcription	Primary neutrophils fromperipheralblood	blood
42	chr5:59938000-59942600	Strong transcription	Monocytes-CD14+_RO01746	blood
43	chr5:59938200-59940600	Strong transcription	A549	lung
44	chr5:59938600-59945200	Weak transcription	Fetal Kidney	kidney
45	chr5:59938800-59943000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr5:59939400-59942400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr5:59939600-59940600	Strong transcription	H1 Cell Line	embryonic stem cell
48	chr5:59939800-59940600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr5:59939800-59940600	Strong transcription	K562	blood
50	chr5:59939800-59942800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links