Variant report

Variant	rs59816625
Chromosome Location	chr2:99878132-99878133
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 67 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs11123775	0.97[AFR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11123777	0.88[ASN][1000 genomes]
rs11123779	0.88[ASN][1000 genomes]
rs11123782	0.82[ASN][1000 genomes]
rs11676581	0.88[ASN][1000 genomes]
rs11685870	0.87[ASN][1000 genomes]
rs11686535	0.82[ASN][1000 genomes]
rs11687328	0.86[ASN][1000 genomes]
rs11892472	0.80[ASN][1000 genomes]
rs11895206	0.82[ASN][1000 genomes]
rs12464785	0.82[ASN][1000 genomes]
rs12475639	0.84[ASN][1000 genomes]
rs13004376	0.85[ASN][1000 genomes]
rs13008948	0.82[ASN][1000 genomes]
rs13009884	0.88[ASN][1000 genomes]
rs13010416	0.88[ASN][1000 genomes]
rs13011240	0.88[ASN][1000 genomes]
rs13016182	0.88[ASN][1000 genomes]
rs13019192	0.80[ASN][1000 genomes]
rs13026997	0.82[ASN][1000 genomes]
rs13033740	0.88[ASN][1000 genomes]
rs17022433	0.98[AFR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17022564	0.82[ASN][1000 genomes]
rs1825770	0.88[ASN][1000 genomes]
rs1955393	0.98[AFR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4850899	0.88[ASN][1000 genomes]
rs55815229	0.82[ASN][1000 genomes]
rs55991925	0.95[AFR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs57242893	0.82[ASN][1000 genomes]
rs58086269	0.81[ASN][1000 genomes]
rs59661148	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62153855	0.81[ASN][1000 genomes]
rs6711977	0.88[ASN][1000 genomes]
rs6732397	0.87[ASN][1000 genomes]
rs6735381	0.88[ASN][1000 genomes]
rs6753588	0.80[ASN][1000 genomes]
rs7421284	0.94[AFR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7561616	0.88[ASN][1000 genomes]
rs7570978	0.87[ASN][1000 genomes]
rs901596	0.98[AFR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:27 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv431424	chr2:99652682-100494682	Flanking Active TSS Enhancers Strong transcription Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
2	nsv961842	chr2:99781138-99886836	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
3	nsv515702	chr2:99827733-99922967	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
4	nsv458685	chr2:99827733-99922967	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
5	nsv582519	chr2:99827733-99922967	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
6	nsv874698	chr2:99827733-99924918	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
7	nsv1001784	chr2:99838079-99910328	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
8	nsv535840	chr2:99838079-99910328	Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Strong transcription Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
9	nsv458696	chr2:99838203-99922967	ZNF genes & repeats Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
10	nsv582520	chr2:99838203-99922967	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
11	nsv997436	chr2:99840131-99916886	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
12	nsv1009872	chr2:99840131-99924543	Weak transcription ZNF genes & repeats Enhancers Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
13	nsv1001194	chr2:99840131-99928323	Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
14	esv2762746	chr2:99840143-99916898	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
15	nsv1005118	chr2:99841951-99924543	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
16	nsv1001736	chr2:99846306-99916886	Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
17	nsv1009459	chr2:99846306-99918895	Enhancers ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
18	nsv1002169	chr2:99846306-99924543	Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
19	esv2751904	chr2:99847882-99913998	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
20	nsv1001235	chr2:99847890-99913998	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
21	nsv582521	chr2:99847890-99922967	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
22	nsv1007566	chr2:99847890-99924543	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
23	nsv999059	chr2:99847890-99926934	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
24	nsv1007249	chr2:99855978-99916886	ZNF genes & repeats Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
25	nsv1004291	chr2:99855978-99919999	Weak transcription Enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
26	nsv1010419	chr2:99857259-99897312	Active TSS Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
27	nsv1003262	chr2:99858556-99924543	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs59816625	LYG1	cis	Skin Sun Exposed Lower leg	GTEx
rs59816625	LYG1	cis	Nerve Tibial	GTEx
rs59816625	REV1	Cis_1M	lymphoblastoid	RTeQTL
rs59816625	LYG1	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:99860400-99899800	Weak transcription	Psoas Muscle	Psoas
2	chr2:99861200-99879200	Weak transcription	Stomach Smooth Muscle	stomach
3	chr2:99861200-99900800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr2:99861800-99899400	Weak transcription	Skeletal Muscle Male	skeletal muscle
5	chr2:99862000-99879200	Weak transcription	Duodenum Smooth Muscle	Duodenum
6	chr2:99869800-99880000	Weak transcription	Right Ventricle	heart
7	chr2:99873800-99900600	Weak transcription	Ovary	ovary
8	chr2:99874600-99879400	Weak transcription	Aorta	Aorta
9	chr2:99876200-99882400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
10	chr2:99877200-99880200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr2:99877600-99878200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr2:99877600-99878200	Enhancers	HMEC	breast
13	chr2:99877800-99878200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr2:99877800-99882200	Weak transcription	Esophagus	oesophagus

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