Variant report

Variant	rs933335
Chromosome Location	chr16:74805668-74805669
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 39 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs12444462	0.86[GIH][hapmap]
rs4888283	1.00[JPT][hapmap];0.85[MEX][hapmap]
rs4888284	1.00[JPT][hapmap];0.80[MEX][hapmap]
rs57113459	0.89[ASN][1000 genomes]
rs57276041	0.94[ASN][1000 genomes]
rs57820954	0.94[ASN][1000 genomes]
rs57832954	0.94[ASN][1000 genomes]
rs57846685	0.94[ASN][1000 genomes]
rs61439639	0.83[ASN][1000 genomes]
rs6564168	1.00[JPT][hapmap];0.80[MEX][hapmap]
rs7189427	0.94[ASN][1000 genomes]
rs7206186	0.94[ASN][1000 genomes]
rs73616419	0.94[ASN][1000 genomes]
rs73616433	0.94[ASN][1000 genomes]
rs73616447	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73616448	0.94[ASN][1000 genomes]
rs73616461	0.94[ASN][1000 genomes]
rs73616476	0.83[ASN][1000 genomes]
rs8048578	1.00[JPT][hapmap];0.85[MEX][hapmap]
rs8055156	1.00[JPT][hapmap]
rs8055626	0.94[ASN][1000 genomes]
rs8060979	1.00[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8061027	0.94[ASN][1000 genomes]
rs929881	0.83[CHD][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs933334	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9931439	1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916687	chr16:74241238-74896721	Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Strong transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	102 gene(s)	inside rSNPs	diseases
2	nsv949374	chr16:74466960-75172358	Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
3	nsv1061095	chr16:74519718-75407020	Strong transcription Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	123 gene(s)	inside rSNPs	diseases
4	nsv1061948	chr16:74660609-74882915	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	67 gene(s)	inside rSNPs	diseases
5	nsv542957	chr16:74660609-74882915	Enhancers Genic enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	67 gene(s)	inside rSNPs	diseases
6	nsv906906	chr16:74664743-74805668	Active TSS Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	57 gene(s)	inside rSNPs	diseases
7	nsv532560	chr16:74692406-75411912	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	111 gene(s)	inside rSNPs	diseases
8	nsv517513	chr16:74743736-74812676	Enhancers Weak transcription Bivalent/Poised TSS Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	36 gene(s)	inside rSNPs	diseases
9	nsv1058900	chr16:74753819-75005050	Weak transcription Strong transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
10	nsv542958	chr16:74753819-75005050	Weak transcription Bivalent Enhancer Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
11	esv3345041	chr16:74756263-75066969	Active TSS Genic enhancers Bivalent/Poised TSS Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	52 gene(s)	inside rSNPs	diseases
12	nsv457520	chr16:74758984-74907440	Bivalent Enhancer Enhancers Flanking Active TSS Genic enhancers Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
13	nsv572976	chr16:74758984-74907440	Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Weak transcription Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs933335	LDHD	cis	cerebellum	SCAN

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:74796200-74807400	Weak transcription	A549	lung
2	chr16:74801600-74807600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr16:74803000-74806400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr16:74804000-74807400	Weak transcription	Pancreas	Pancrea
5	chr16:74804200-74807400	Weak transcription	Fetal Intestine Small	intestine
6	chr16:74804200-74807400	Weak transcription	Gastric	stomach
7	chr16:74804200-74807400	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr16:74804600-74805800	Enhancers	Duodenum Mucosa	Duodenum
9	chr16:74804600-74806000	Enhancers	Hela-S3	cervix
10	chr16:74804600-74806600	Enhancers	Primary B cells from peripheral blood	blood
11	chr16:74804800-74805800	Enhancers	Brain Inferior Temporal Lobe	brain
12	chr16:74805200-74805800	Enhancers	Rectal Mucosa Donor 29	rectum
13	chr16:74805400-74805800	Flanking Active TSS	Brain Hippocampus Middle	brain
14	chr16:74805400-74806200	Enhancers	Primary B cells from cord blood	blood
15	chr16:74805600-74805800	Flanking Active TSS	Brain Cingulate Gyrus	brain
16	chr16:74805600-74805800	Flanking Active TSS	Brain Substantia Nigra	brain
17	chr16:74805600-74805800	Bivalent Enhancer	Fetal Muscle Trunk	muscle
18	chr16:74805600-74806000	Enhancers	Brain Anterior Caudate	brain
19	chr16:74805600-74806400	Flanking Active TSS	GM12878-XiMat	blood
20	chr16:74805600-74806800	Weak transcription	Stomach Mucosa	stomach
21	chr16:74805600-74806800	Enhancers	Thymus	Thymus
22	chr16:74805600-74807400	Weak transcription	Colonic Mucosa	Colon
23	chr16:74805600-74807400	Enhancers	Fetal Thymus	thymus
24	chr16:74805600-74809000	Active TSS	Brain Angular Gyrus	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links