Variant report

Variant	rs4357030
Chromosome Location	chr5:124316031-124316032
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:124314982..124317852-chr5:124324896..124327856,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RP11-43D2.2.1-10	chr5:124315897-124317909	XLOC_004536

Extended variants
information (count: 35 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10044837	0.93[ASN][1000 genomes]
rs10055285	0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10057766	0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10060023	0.91[ASN][1000 genomes]
rs10079602	0.91[ASN][1000 genomes]
rs11241779	0.83[ASN][1000 genomes]
rs11743521	0.80[ASN][1000 genomes]
rs11951671	0.83[ASN][1000 genomes]
rs11958289	0.82[ASN][1000 genomes]
rs12109265	0.90[ASN][1000 genomes]
rs13158867	0.81[ASN][1000 genomes]
rs1374130	0.90[ASN][1000 genomes]
rs17152193	0.89[ASN][1000 genomes]
rs35862376	0.82[ASN][1000 genomes]
rs36041674	0.80[ASN][1000 genomes]
rs4240384	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4240385	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4311414	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4331894	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4540171	0.90[ASN][1000 genomes]
rs6861021	0.91[ASN][1000 genomes]
rs6861089	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6863192	0.90[ASN][1000 genomes]
rs6869863	0.81[ASN][1000 genomes]
rs6872411	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6875187	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6875763	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6876036	0.90[ASN][1000 genomes]
rs6895658	0.81[ASN][1000 genomes]
rs6898265	0.81[CHB][hapmap]
rs7732618	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9968605	0.82[EUR][1000 genomes];0.91[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	nsv882822	chr5:124250018-124449375	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv830474	chr5:124263628-124431299	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv599657	chr5:124284253-124330522	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Strong transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4357030	NA	cis	multi-tissue	Pritchard
rs4357030	SNX2	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:124311200-124316400	Weak transcription	Pancreas	Pancrea
2	chr5:124312400-124316200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr5:124313000-124317200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr5:124314400-124316400	Enhancers	Fetal Stomach	stomach
5	chr5:124314400-124316600	Enhancers	H1 Cell Line	embryonic stem cell
6	chr5:124314400-124316600	Enhancers	Placenta Amnion	Placenta Amnion
7	chr5:124314400-124317000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr5:124314400-124317200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr5:124314400-124317400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr5:124314400-124317400	Enhancers	HUES6 Cell Line	embryonic stem cell
11	chr5:124314400-124317600	Enhancers	Fetal Brain Male	brain
12	chr5:124314400-124317600	Enhancers	Fetal Lung	lung
13	chr5:124314400-124318400	Enhancers	Stomach Mucosa	stomach
14	chr5:124314400-124318600	Enhancers	Fetal Intestine Small	intestine
15	chr5:124314600-124316400	Enhancers	Brain Germinal Matrix	brain
16	chr5:124314600-124317000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr5:124314600-124317200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr5:124314600-124317200	Enhancers	iPS-15b Cell Line	embryonic stem cell
19	chr5:124314600-124318000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr5:124314600-124318400	Enhancers	Primary B cells from peripheral blood	blood
21	chr5:124314600-124318400	Enhancers	Fetal Intestine Large	intestine
22	chr5:124314800-124317200	Enhancers	Brain Anterior Caudate	brain
23	chr5:124314800-124317200	Enhancers	Brain Hippocampus Middle	brain
24	chr5:124314800-124317400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
25	chr5:124314800-124317400	Enhancers	Cortex derived primary cultured neurospheres	brain
26	chr5:124314800-124318000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr5:124314800-124318400	Enhancers	Dnd41	blood
28	chr5:124315000-124316800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
29	chr5:124315000-124318400	Enhancers	Primary B cells from cord blood	blood
30	chr5:124315000-124319000	Enhancers	Breast Myoepithelial Primary Cells	Breast
31	chr5:124315200-124316200	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
32	chr5:124315200-124316200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr5:124315200-124316200	Weak transcription	HMEC	breast
34	chr5:124315200-124316400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr5:124315200-124316600	Weak transcription	Fetal Kidney	kidney
36	chr5:124315200-124317000	Enhancers	Brain Cingulate Gyrus	brain
37	chr5:124315200-124317200	Enhancers	Brain Substantia Nigra	brain
38	chr5:124315200-124317200	Weak transcription	Duodenum Mucosa	Duodenum
39	chr5:124315200-124317400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr5:124315200-124317400	Weak transcription	Sigmoid Colon	Sigmoid Colon
41	chr5:124315200-124317800	Weak transcription	Fetal Muscle Leg	muscle
42	chr5:124315400-124316400	Weak transcription	Pancreatic Islets	Pancreatic Islet
43	chr5:124315400-124316800	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
44	chr5:124315400-124317200	Weak transcription	Gastric	stomach
45	chr5:124315600-124316200	Enhancers	GM12878-XiMat	blood
46	chr5:124315600-124316400	Weak transcription	Fetal Brain Female	brain
47	chr5:124315600-124316600	Weak transcription	Brain Inferior Temporal Lobe	brain
48	chr5:124315600-124317000	Enhancers	Brain Angular Gyrus	brain
49	chr5:124315600-124317400	Weak transcription	H9 Cell Line	embryonic stem cell
50	chr5:124315800-124316600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin

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