Variant report

Variant	rs13006841
Chromosome Location	chr2:40458140-40458141
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	chr2:40457676..40460307-chr2:40464951..40466510,2	K562	blood:

Extended variants
information (count: 104 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:92)

rs_ID	r²[population]
rs10153786	0.83[AMR][1000 genomes]
rs10167744	0.86[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs10167955	0.84[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs10175778	1.00[ASN][1000 genomes]
rs10176352	1.00[ASN][1000 genomes]
rs10176641	1.00[ASN][1000 genomes]
rs10183585	0.86[ASW][hapmap];1.00[CHD][hapmap];0.83[LWK][hapmap];0.86[MEX][hapmap];0.92[MKK][hapmap];0.94[YRI][hapmap];0.89[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs10199306	1.00[ASN][1000 genomes]
rs10207018	1.00[ASN][1000 genomes]
rs10207038	1.00[ASN][1000 genomes]
rs10490207	1.00[ASN][1000 genomes]
rs11884718	1.00[ASN][1000 genomes]
rs11884732	1.00[ASN][1000 genomes]
rs11885401	1.00[ASN][1000 genomes]
rs11887546	1.00[ASN][1000 genomes]
rs11887643	1.00[ASN][1000 genomes]
rs11889015	0.86[ASW][hapmap];1.00[CHD][hapmap];0.86[MEX][hapmap];0.92[MKK][hapmap];0.88[YRI][hapmap];0.82[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs11890878	0.89[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs11891508	0.89[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs11891921	1.00[ASN][1000 genomes]
rs11894296	1.00[CEU][hapmap];0.83[YRI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11894882	1.00[ASN][1000 genomes]
rs11895025	1.00[CHD][hapmap];0.88[MEX][hapmap];0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11899204	1.00[CEU][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11903986	1.00[ASN][1000 genomes]
rs12329007	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs13383126	1.00[ASN][1000 genomes]
rs13384452	1.00[ASN][1000 genomes]
rs13385280	1.00[ASN][1000 genomes]
rs13389962	1.00[ASN][1000 genomes]
rs13398048	1.00[ASN][1000 genomes]
rs13398809	1.00[ASN][1000 genomes]
rs13400484	1.00[ASN][1000 genomes]
rs13408531	1.00[CHD][hapmap];1.00[MEX][hapmap];0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs13414508	0.86[ASW][hapmap];1.00[CHD][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.81[YRI][hapmap];0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs13428581	1.00[ASN][1000 genomes]
rs13428681	1.00[ASN][1000 genomes]
rs1366424	1.00[ASN][1000 genomes]
rs1428574	1.00[ASN][1000 genomes]
rs17025234	1.00[ASN][1000 genomes]
rs17025260	1.00[ASN][1000 genomes]
rs17025271	1.00[ASN][1000 genomes]
rs17025453	1.00[ASN][1000 genomes]
rs17025510	1.00[ASN][1000 genomes]
rs17025570	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17025628	0.88[YRI][hapmap];0.86[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs17038992	1.00[ASN][1000 genomes]
rs17570537	0.94[YRI][hapmap];0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1896712	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2033230	1.00[ASN][1000 genomes]
rs2041827	1.00[ASN][1000 genomes]
rs28380530	1.00[ASN][1000 genomes]
rs28660667	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs374153	1.00[ASN][1000 genomes]
rs390579	1.00[ASN][1000 genomes]
rs400673	1.00[ASN][1000 genomes]
rs405416	1.00[ASN][1000 genomes]
rs423177	1.00[ASN][1000 genomes]
rs440387	1.00[ASN][1000 genomes]
rs6704907	1.00[ASN][1000 genomes]
rs6720270	1.00[ASN][1000 genomes]
rs6728644	1.00[ASN][1000 genomes]
rs6729089	1.00[ASN][1000 genomes]
rs6758015	1.00[ASN][1000 genomes]
rs6760003	1.00[ASN][1000 genomes]
rs71439287	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73924568	1.00[ASN][1000 genomes]
rs73924573	1.00[ASN][1000 genomes]
rs73926129	0.91[AFR][1000 genomes]
rs73926130	0.91[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs73927124	1.00[ASN][1000 genomes]
rs741320	1.00[ASN][1000 genomes]
rs7562916	1.00[ASN][1000 genomes]
rs7563045	1.00[ASN][1000 genomes]
rs7563290	1.00[ASN][1000 genomes]
rs7563445	0.94[YRI][hapmap];0.91[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7567178	1.00[ASN][1000 genomes]
rs7570501	1.00[ASN][1000 genomes]
rs7570522	1.00[ASN][1000 genomes]
rs7575693	1.00[ASN][1000 genomes]
rs7575802	1.00[ASN][1000 genomes]
rs7583602	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7589951	1.00[ASN][1000 genomes]
rs7601672	1.00[ASN][1000 genomes]
rs7601991	1.00[ASN][1000 genomes]
rs7602006	1.00[ASN][1000 genomes]
rs7602342	1.00[ASN][1000 genomes]
rs7602377	1.00[ASN][1000 genomes]
rs7605482	0.86[ASW][hapmap];1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs7607992	1.00[ASN][1000 genomes]
rs9309053	1.00[ASN][1000 genomes]
rs9653516	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529606	chr2:40206280-40896881	Flanking Active TSS Enhancers Active TSS Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv873902	chr2:40231282-40466268	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	nsv1000572	chr2:40271958-40458911	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv535654	chr2:40271958-40458911	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv581502	chr2:40273903-40459645	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv873904	chr2:40292289-40466268	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	nsv873910	chr2:40391907-40466268	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
8	esv1851152	chr2:40393223-40512023	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
9	nsv873911	chr2:40423454-41161464	ZNF genes & repeats Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
10	nsv1008190	chr2:40429442-40506772	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
11	esv34071	chr2:40435231-40578229	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
12	nsv524586	chr2:40447587-40497501	Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13006841	GALM	cis	parietal	SCAN

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:40448000-40487400	Weak transcription	Monocytes-CD14+_RO01746	blood
2	chr2:40451400-40490000	Weak transcription	Dnd41	blood
3	chr2:40453600-40459400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr2:40453800-40471000	Weak transcription	Right Ventricle	heart
5	chr2:40453800-40471400	Weak transcription	Right Atrium	heart
6	chr2:40454400-40458200	Weak transcription	Rectal Smooth Muscle	rectum
7	chr2:40454600-40459200	Enhancers	Fetal Heart	heart
8	chr2:40455600-40466600	Weak transcription	Muscle Satellite Cultured Cells	--
9	chr2:40456000-40458200	Weak transcription	Fetal Muscle Leg	muscle
10	chr2:40456000-40466600	Weak transcription	Left Ventricle	heart
11	chr2:40456400-40466800	Weak transcription	HSMM	muscle
12	chr2:40457200-40459400	Enhancers	Fetal Thymus	thymus
13	chr2:40457400-40458200	Enhancers	Brain Angular Gyrus	brain
14	chr2:40457600-40458400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr2:40458000-40458200	Enhancers	Stomach Smooth Muscle	stomach
16	chr2:40458000-40458600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin

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