Variant report

Variant	rs337689
Chromosome Location	chr5:113723619-113723620
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:113716230..113718820-chr5:113722226..113724682,2	K562	blood:

Extended variants
information (count: 63 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs1013168	1.00[JPT][hapmap]
rs1072922	0.88[JPT][hapmap]
rs12188044	0.86[JPT][hapmap]
rs13155731	0.88[JPT][hapmap]
rs13163662	0.88[JPT][hapmap]
rs13173796	0.88[JPT][hapmap]
rs13174521	0.88[JPT][hapmap]
rs13176052	0.83[CHB][hapmap];0.88[JPT][hapmap]
rs13179135	0.86[JPT][hapmap]
rs13181189	0.86[JPT][hapmap]
rs13183393	0.88[JPT][hapmap]
rs13184658	0.83[CHB][hapmap];0.88[JPT][hapmap]
rs13186627	0.88[JPT][hapmap]
rs13187753	0.88[JPT][hapmap]
rs13190428	0.88[JPT][hapmap]
rs1457760	0.83[CHB][hapmap];0.88[JPT][hapmap]
rs1457761	1.00[CEU][hapmap];0.91[CHB][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1457762	0.85[CEU][hapmap];0.83[CHB][hapmap];0.84[GIH][hapmap];0.88[JPT][hapmap]
rs1496390	0.83[CHB][hapmap]
rs163210	0.88[JPT][hapmap]
rs163211	0.92[ASN][1000 genomes]
rs168090	1.00[JPT][hapmap];0.81[YRI][hapmap];0.85[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs181949	0.92[CHB][hapmap]
rs2125146	0.88[JPT][hapmap]
rs337683	0.81[ASW][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];0.81[YRI][hapmap];0.82[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs337684	0.84[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs337685	1.00[CEU][hapmap];0.92[CHB][hapmap];0.93[GIH][hapmap];0.88[JPT][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs337691	1.00[CEU][hapmap];0.92[CHB][hapmap];0.93[GIH][hapmap];0.88[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs337695	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs337699	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs337704	0.84[ASN][1000 genomes]
rs337705	0.83[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs337707	0.81[CEU][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.92[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs337708	1.00[JPT][hapmap];0.86[YRI][hapmap];0.89[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs337709	0.81[CEU][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs337710	0.92[ASN][1000 genomes]
rs337711	0.88[JPT][hapmap]
rs337712	0.92[ASN][1000 genomes]
rs337714	0.87[ASW][hapmap];0.85[CHB][hapmap];1.00[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.92[ASN][1000 genomes]
rs338622	0.94[YRI][hapmap];0.89[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs338623	0.84[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs338625	0.93[ASW][hapmap];0.81[CEU][hapmap];0.85[CHB][hapmap];1.00[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.83[MEX][hapmap];0.81[YRI][hapmap];0.88[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs338663	0.89[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs338664	0.83[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs338666	0.89[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs36137318	0.82[ASN][1000 genomes]
rs36938	1.00[CHB][hapmap]
rs36942	0.92[CHB][hapmap]
rs36945	0.92[CHB][hapmap]
rs36946	1.00[CHB][hapmap];0.83[CHD][hapmap];0.84[MEX][hapmap];0.81[ASN][1000 genomes]
rs36947	0.92[ASN][1000 genomes]
rs36949	0.92[CHB][hapmap];0.88[JPT][hapmap]
rs36950	0.92[CHB][hapmap];0.88[JPT][hapmap]
rs3857431	0.88[JPT][hapmap]
rs388084	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4705504	0.88[JPT][hapmap]
rs4705665	0.88[JPT][hapmap]
rs4705667	1.00[JPT][hapmap]
rs4705668	0.88[JPT][hapmap]
rs6859284	0.87[ASW][hapmap];0.85[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs921981	0.89[AFR][1000 genomes];0.92[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	nsv882728	chr5:113651694-113731423	Bivalent/Poised TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
2	nsv830451	chr5:113684301-113829833	Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs337689	COMMD10	cis	parietal	SCAN
rs337689	CCDC112	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:113713200-113730800	Weak transcription	Brain Anterior Caudate	brain
2	chr5:113715000-113723800	Weak transcription	H1 Cell Line	embryonic stem cell
3	chr5:113715000-113727800	Weak transcription	HUES6 Cell Line	embryonic stem cell
4	chr5:113721800-113725000	Enhancers	iPS-18 Cell Line	embryonic stem cell
5	chr5:113722000-113725400	Enhancers	HUES48 Cell Line	embryonic stem cell
6	chr5:113722200-113725200	Enhancers	HUES64 Cell Line	embryonic stem cell
7	chr5:113722400-113723800	Enhancers	ES-I3 Cell Line	embryonic stem cell
8	chr5:113722400-113724200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
9	chr5:113722400-113724400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr5:113722400-113724800	Enhancers	Liver	Liver
11	chr5:113722400-113725000	Enhancers	iPS-15b Cell Line	embryonic stem cell
12	chr5:113722600-113725200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr5:113722800-113723800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr5:113722800-113725000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr5:113722800-113725600	Enhancers	Cortex derived primary cultured neurospheres	brain
16	chr5:113723000-113723800	Enhancers	Brain Hippocampus Middle	brain
17	chr5:113723000-113725000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr5:113723600-113723800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr5:113723600-113723800	Enhancers	Brain Cingulate Gyrus	brain
20	chr5:113723600-113724600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
21	chr5:113723600-113725400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland

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