Variant report

Variant	rs257621
Chromosome Location	chr16:58761580-58761581
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	chr16:58761095..58764938-chr16:58766289..58768902,3	K562	blood:

Variant related genes	Relation type
ENSG00000125166	Chromatin interaction
ENSG00000245768	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs1058192	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11076262	0.96[CEU][hapmap];0.97[TSI][hapmap]
rs14221	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1424245	0.92[ASN][1000 genomes]
rs1436429	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs149479	0.90[AMR][1000 genomes]
rs154435	0.83[AMR][1000 genomes]
rs1595181	0.96[CEU][hapmap];0.97[TSI][hapmap]
rs1616798	0.81[JPT][hapmap]
rs1618602	0.84[JPT][hapmap]
rs1646256	0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs1646260	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1646267	0.85[EUR][1000 genomes]
rs1657176	0.82[EUR][1000 genomes]
rs1657177	0.82[EUR][1000 genomes]
rs1657178	0.81[JPT][hapmap];0.83[EUR][1000 genomes]
rs1657179	0.81[JPT][hapmap]
rs171786	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[MKK][hapmap];0.95[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs173992	0.91[EUR][1000 genomes]
rs183757	0.92[EUR][1000 genomes]
rs185397	0.81[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.95[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs187277	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs190473	0.82[EUR][1000 genomes]
rs257616	0.81[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.95[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs257617	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs257618	0.84[CEU][hapmap];0.85[EUR][1000 genomes]
rs257619	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs257620	0.81[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.95[YRI][hapmap]
rs257630	0.92[CEU][hapmap];0.97[TSI][hapmap];0.92[EUR][1000 genomes]
rs257631	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs257632	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs257633	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs257634	0.85[EUR][1000 genomes]
rs257636	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs257637	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs257638	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs257650	0.89[AMR][1000 genomes]
rs30834	0.91[AMR][1000 genomes]
rs30836	0.83[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs30837	0.91[AMR][1000 genomes]
rs30838	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs30840	0.91[AMR][1000 genomes]
rs30841	0.91[AMR][1000 genomes]
rs30842	1.00[MEX][hapmap];0.91[AMR][1000 genomes]
rs40575	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4238801	0.90[JPT][hapmap];0.82[MEX][hapmap]
rs4575523	0.90[JPT][hapmap];0.81[MEX][hapmap]
rs7188608	0.81[EUR][1000 genomes]
rs8046154	0.84[JPT][hapmap];0.81[MEX][hapmap]
rs839418	0.91[AMR][1000 genomes]
rs863944	0.84[CEU][hapmap];0.92[TSI][hapmap];0.85[EUR][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	esv2758427	chr16:58579005-58876037	Enhancers Strong transcription Genic enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	esv2758650	chr16:58579005-58876037	ZNF genes & repeats Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
3	nsv510686	chr16:58646119-58765894	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
4	nsv1065296	chr16:58738198-58837859	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	n/a
5	nsv1065269	chr16:58743487-58972224	Flanking Active TSS Enhancers Strong transcription Active TSS Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs257621	GOT2	cis	Thyroid	GTEx
rs257621	GOT2	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:58738400-58766600	Weak transcription	Stomach Mucosa	stomach
2	chr16:58747800-58767000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr16:58752600-58766600	Weak transcription	NHLF	lung
4	chr16:58753000-58766000	Weak transcription	Small Intestine	intestine
5	chr16:58753200-58765600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
6	chr16:58753200-58766400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr16:58753200-58766600	Weak transcription	Rectal Smooth Muscle	rectum
8	chr16:58753200-58766800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr16:58753400-58766400	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr16:58754000-58766800	Weak transcription	Esophagus	oesophagus
11	chr16:58755200-58766800	Weak transcription	Fetal Lung	lung
12	chr16:58755400-58766800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr16:58755600-58764200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
14	chr16:58755600-58766400	Weak transcription	Fetal Brain Male	brain
15	chr16:58756200-58764200	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr16:58756200-58766800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr16:58756200-58766800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr16:58756200-58766800	Weak transcription	Placenta Amnion	Placenta Amnion
19	chr16:58756400-58761600	Weak transcription	Spleen	Spleen
20	chr16:58756400-58766400	Weak transcription	Rectal Mucosa Donor 31	rectum
21	chr16:58757000-58766200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr16:58757000-58766600	Weak transcription	Colonic Mucosa	Colon
23	chr16:58757000-58767400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr16:58757200-58761600	Weak transcription	Skeletal Muscle Female	skeletal muscle
25	chr16:58757200-58766600	Weak transcription	Brain Germinal Matrix	brain
26	chr16:58757400-58765600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
27	chr16:58757400-58766200	Weak transcription	Muscle Satellite Cultured Cells	--
28	chr16:58757600-58761600	Weak transcription	Skeletal Muscle Male	skeletal muscle
29	chr16:58757600-58761600	Weak transcription	GM12878-XiMat	blood
30	chr16:58757600-58763000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
31	chr16:58757600-58764000	Weak transcription	Brain Inferior Temporal Lobe	brain
32	chr16:58757600-58765600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr16:58757600-58766200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr16:58757600-58766200	Weak transcription	A549	lung
35	chr16:58757600-58766200	Weak transcription	NH-A	brain
36	chr16:58757600-58766600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr16:58757600-58766600	Weak transcription	Rectal Mucosa Donor 29	rectum
38	chr16:58757600-58767000	Weak transcription	Primary monocytes fromperipheralblood	blood
39	chr16:58757800-58761600	Weak transcription	Primary B cells from cord blood	blood
40	chr16:58757800-58761600	Weak transcription	Brain Angular Gyrus	brain
41	chr16:58757800-58761600	Weak transcription	Fetal Thymus	thymus
42	chr16:58757800-58762400	Weak transcription	Brain Hippocampus Middle	brain
43	chr16:58757800-58762400	Weak transcription	Stomach Smooth Muscle	stomach
44	chr16:58757800-58762600	Weak transcription	Fetal Muscle Leg	muscle
45	chr16:58757800-58763000	Weak transcription	Brain Cingulate Gyrus	brain
46	chr16:58757800-58763200	Weak transcription	Brain Anterior Caudate	brain
47	chr16:58757800-58763400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
48	chr16:58757800-58764000	Weak transcription	HUES48 Cell Line	embryonic stem cell
49	chr16:58757800-58764000	Weak transcription	Primary T helper cells PMA-I stimulated	--
50	chr16:58757800-58764000	Weak transcription	Fetal Intestine Large	intestine

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links