Variant report

Variant	rs13122604
Chromosome Location	chr4:74785503-74785504
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	chr4:74762185..74764051-chr4:74784801..74787079,2	K562	blood:
2	chr4:74780043..74783645-chr4:74784041..74787591,3	K562	blood:

Extended variants
information (count: 66 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs10007249	0.83[ASN][1000 genomes]
rs10017182	0.88[EUR][1000 genomes]
rs10033521	0.89[EUR][1000 genomes]
rs10938105	0.89[EUR][1000 genomes]
rs11729931	0.86[CEU][hapmap]
rs11939236	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12498174	0.88[EUR][1000 genomes]
rs13112134	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13120504	0.87[EUR][1000 genomes]
rs13128887	0.89[EUR][1000 genomes]
rs13136948	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1435521	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs149611	0.86[ASN][1000 genomes]
rs1595008	0.87[EUR][1000 genomes]
rs1595009	0.84[EUR][1000 genomes]
rs2082822	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2082823	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2115695	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2175498	0.87[EUR][1000 genomes]
rs2367443	0.89[EUR][1000 genomes]
rs2472649	0.94[CEU][hapmap]
rs2564596	0.86[EUR][1000 genomes]
rs3114083	0.98[EUR][1000 genomes]
rs352036	0.86[ASN][1000 genomes]
rs353028	0.85[ASN][1000 genomes]
rs353029	0.85[ASN][1000 genomes]
rs353031	0.85[ASN][1000 genomes]
rs353032	0.83[ASN][1000 genomes]
rs353034	0.81[ASN][1000 genomes]
rs353039	0.81[ASN][1000 genomes]
rs353042	0.93[CHB][hapmap];0.92[JPT][hapmap];0.80[MEX][hapmap]
rs3906613	0.89[EUR][1000 genomes]
rs4399951	0.88[EUR][1000 genomes]
rs4694180	0.87[EUR][1000 genomes]
rs4694654	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4694655	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.85[TSI][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4694657	0.89[EUR][1000 genomes]
rs4694658	0.89[EUR][1000 genomes]
rs4694659	0.87[EUR][1000 genomes]
rs4694660	0.86[EUR][1000 genomes]
rs4694661	0.86[EUR][1000 genomes]
rs499141	0.81[ASN][1000 genomes]
rs529312	0.81[ASN][1000 genomes]
rs57274239	0.83[ASN][1000 genomes]
rs585778	0.81[ASN][1000 genomes]
rs629315	0.81[ASN][1000 genomes]
rs6446969	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6446970	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6446973	0.87[EUR][1000 genomes]
rs6810940	0.86[EUR][1000 genomes]
rs6813021	0.86[EUR][1000 genomes]
rs6819077	0.89[EUR][1000 genomes]
rs6819566	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6822890	0.89[EUR][1000 genomes]
rs6832583	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7662553	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7666671	0.80[ASN][1000 genomes]
rs7671525	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8180167	0.89[EUR][1000 genomes]
rs9291189	0.89[EUR][1000 genomes]
rs938094	0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1001725	chr4:74354050-74860924	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv530126	chr4:74376622-74843892	Bivalent Enhancer Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
3	nsv525980	chr4:74731526-75382209	Strong transcription Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
4	nsv1004768	chr4:74774372-75109579	Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
5	nsv1006218	chr4:74782324-75105424	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs13122604	CXCL5	cis	parietal	SCAN
rs13122604	GC	cis	cerebellum	SCAN

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:74781400-74786000	Enhancers	Muscle Satellite Cultured Cells	--
2	chr4:74782400-74786000	Enhancers	HSMM	muscle
3	chr4:74782600-74785800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr4:74784000-74788400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr4:74784200-74785600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr4:74784200-74788200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr4:74784200-74788200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr4:74784200-74788200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr4:74784200-74788600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr4:74784400-74785600	Weak transcription	HMEC	breast
11	chr4:74784600-74788800	Weak transcription	Hela-S3	cervix
12	chr4:74785000-74785600	Enhancers	NHLF	lung
13	chr4:74785200-74785800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr4:74785200-74786000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr4:74785200-74786000	Enhancers	NH-A	brain
16	chr4:74785200-74786000	Enhancers	NHEK	skin
17	chr4:74785400-74785800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr4:74785400-74785800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr4:74785400-74785800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr4:74785400-74786000	Enhancers	HSMMtube	muscle
21	chr4:74785400-74786000	Enhancers	Osteobl	bone

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