Variant report

Variant	rs458275
Chromosome Location	chr11:72335500-72335501
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:72311450..72313060-chr11:72334269..72335781,2	K562	blood:
2	chr11:72313089..72314978-chr11:72334364..72335937,2	K562	blood:
3	chr11:72325202..72330805-chr11:72334238..72338443,6	K562	blood:
4	chr11:72333492..72335782-chr11:72342126..72344876,2	K562	blood:
5	chr11:72334834..72339078-chr11:72340923..72346253,6	K562	blood:
6	chr11:72329305..72334052-chr11:72334284..72337478,5	K562	blood:

Variant related genes	Relation type
ENSG00000272036	Chromatin interaction
ENSG00000251919	Chromatin interaction

Extended variants
information (count: 70 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10793036	0.87[CHB][hapmap];0.89[CHD][hapmap];0.87[JPT][hapmap]
rs11235551	0.86[CHB][hapmap];0.93[JPT][hapmap];0.89[ASN][1000 genomes]
rs11235556	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11235557	0.84[ASN][1000 genomes]
rs11235558	0.84[ASN][1000 genomes]
rs11235559	0.94[CHB][hapmap];0.92[CHD][hapmap];0.81[GIH][hapmap];0.80[MEX][hapmap];0.84[ASN][1000 genomes]
rs1135029	0.81[CHB][hapmap];0.80[JPT][hapmap]
rs12146545	0.94[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs12276767	0.89[ASN][1000 genomes]
rs12362256	0.82[ASN][1000 genomes]
rs12363065	0.94[CHB][hapmap];0.92[CHD][hapmap];0.81[GIH][hapmap];0.84[ASN][1000 genomes]
rs12576058	0.94[CHB][hapmap];0.82[CHD][hapmap]
rs12797368	0.84[ASN][1000 genomes]
rs12797791	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12804316	0.92[CHB][hapmap];0.84[ASN][1000 genomes]
rs1391888	0.94[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs1467135	0.81[CHB][hapmap];0.80[JPT][hapmap]
rs163694	0.94[CHB][hapmap]
rs1872126	0.94[CHB][hapmap];0.82[CHD][hapmap]
rs189332	0.94[CHB][hapmap];0.90[CHD][hapmap];0.80[MEX][hapmap];0.83[ASN][1000 genomes]
rs1980089	0.80[JPT][hapmap]
rs1980090	0.80[JPT][hapmap]
rs2035467	0.94[CHB][hapmap];0.83[ASN][1000 genomes]
rs2037030	0.84[ASN][1000 genomes]
rs2306609	0.80[CHB][hapmap]
rs341049	0.81[CHB][hapmap];0.80[JPT][hapmap]
rs341051	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs341052	1.00[CHB][hapmap];0.93[JPT][hapmap];0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs341053	0.94[CHB][hapmap];0.82[CHD][hapmap]
rs341060	0.83[ASN][1000 genomes]
rs341061	0.93[CHB][hapmap];0.88[CHD][hapmap];0.83[ASN][1000 genomes]
rs341062	0.82[ASN][1000 genomes]
rs341086	0.81[CHB][hapmap];0.89[CHD][hapmap];0.87[JPT][hapmap]
rs342322	0.84[ASN][1000 genomes]
rs3781913	0.94[CHB][hapmap];0.90[CHD][hapmap];0.84[ASN][1000 genomes]
rs3781916	0.93[CHB][hapmap];0.84[ASN][1000 genomes]
rs3781939	0.81[CHB][hapmap];0.80[JPT][hapmap]
rs3825009	0.86[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs401801	0.93[CEU][hapmap];0.81[CHB][hapmap];0.87[JPT][hapmap];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs455611	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs456405	0.84[CHB][hapmap];0.85[JPT][hapmap];0.85[ASN][1000 genomes]
rs458575	0.87[CHB][hapmap];0.87[CHD][hapmap];0.94[JPT][hapmap];0.89[ASN][1000 genomes]
rs4943939	0.81[CHB][hapmap];0.87[JPT][hapmap]
rs56133505	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61895572	0.89[ASN][1000 genomes]
rs7105428	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7119321	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs900613	0.87[CHB][hapmap]
rs900614	0.86[CHB][hapmap]
rs90409	0.86[CHB][hapmap];0.85[JPT][hapmap]
rs907853	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs907854	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs907856	0.95[ASN][1000 genomes]
rs907857	0.95[ASN][1000 genomes]
rs907858	0.95[ASN][1000 genomes]
rs932074	0.96[ASN][1000 genomes]
rs932075	0.96[ASN][1000 genomes]

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	esv1806140	chr11:72268466-72546175	Enhancers Transcr. at gene 5' and 3' Strong transcription Genic enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	77 gene(s)	inside rSNPs	diseases
2	esv1832864	chr11:72270965-72389125	Bivalent Enhancer Bivalent/Poised TSS Active TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	19 gene(s)	inside rSNPs	diseases
3	nsv832207	chr11:72272750-72469122	Weak transcription Bivalent Enhancer Enhancers Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	31 gene(s)	inside rSNPs	diseases
4	nsv468633	chr11:72281884-72336564	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Strong transcription Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	15 gene(s)	inside rSNPs	diseases
5	nsv468634	chr11:72281884-72336564	Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	15 gene(s)	inside rSNPs	diseases
6	nsv555406	chr11:72281884-72336564	Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	15 gene(s)	inside rSNPs	diseases
7	nsv523601	chr11:72281884-72430935	Enhancers Genic enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	24 gene(s)	inside rSNPs	diseases
8	nsv468635	chr11:72284569-72336564	Weak transcription Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	11 gene(s)	inside rSNPs	diseases
9	nsv555407	chr11:72284569-72336564	Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Genic enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	11 gene(s)	inside rSNPs	diseases
10	nsv1042182	chr11:72294042-72348491	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	11 gene(s)	inside rSNPs	diseases
11	nsv825991	chr11:72320642-72385221	Genic enhancers Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	11 gene(s)	inside rSNPs	diseases
12	esv3394774	chr11:72320884-72694077	Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
13	esv3441775	chr11:72333404-72337902	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs458275	FOLR3	cis	parietal	SCAN
rs458275	GDPD5	cis	parietal	SCAN

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:72327600-72335600	Weak transcription	Esophagus	oesophagus
2	chr11:72329200-72335600	Weak transcription	Brain Substantia Nigra	brain
3	chr11:72329400-72335800	Weak transcription	Brain Hippocampus Middle	brain
4	chr11:72329600-72336000	Weak transcription	Brain Germinal Matrix	brain
5	chr11:72330600-72335600	Weak transcription	Colon Smooth Muscle	Colon
6	chr11:72330600-72335600	Weak transcription	Rectal Smooth Muscle	rectum
7	chr11:72330600-72335800	Weak transcription	Fetal Muscle Trunk	muscle
8	chr11:72330600-72336200	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr11:72331200-72335600	Weak transcription	Brain Cingulate Gyrus	brain
10	chr11:72331200-72335600	Weak transcription	Right Ventricle	heart
11	chr11:72331400-72335800	Weak transcription	Fetal Brain Male	brain
12	chr11:72331400-72341200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr11:72331600-72335600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr11:72331600-72336800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr11:72332200-72336000	Weak transcription	Fetal Stomach	stomach
16	chr11:72332200-72336200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr11:72332600-72335600	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr11:72332800-72335600	Weak transcription	Pancreas	Pancrea
19	chr11:72333600-72335800	Weak transcription	Primary B cells from peripheral blood	blood
20	chr11:72334200-72341600	Enhancers	Right Atrium	heart
21	chr11:72334400-72338800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
22	chr11:72334800-72350200	Enhancers	Left Ventricle	heart
23	chr11:72335400-72335600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr11:72335400-72335600	Enhancers	Adipose Nuclei	Adipose
25	chr11:72335400-72335600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
26	chr11:72335400-72335600	Bivalent Enhancer	K562	blood
27	chr11:72335400-72335800	Enhancers	Fetal Kidney	kidney
28	chr11:72335400-72336000	Genic enhancers	Duodenum Mucosa	Duodenum
29	chr11:72335400-72336000	Genic enhancers	Stomach Smooth Muscle	stomach
30	chr11:72335400-72336000	Enhancers	Spleen	Spleen
31	chr11:72335400-72337200	Enhancers	Primary hematopoietic stem cells	blood
32	chr11:72335400-72337800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr11:72335400-72337800	Enhancers	Gastric	stomach
34	chr11:72335400-72338000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr11:72335400-72338000	Enhancers	Fetal Intestine Small	intestine
36	chr11:72335400-72338400	Enhancers	HUVEC	blood vessel
37	chr11:72335400-72340000	Enhancers	Fetal Brain Female	brain
38	chr11:72335400-72340200	Enhancers	Skeletal Muscle Female	skeletal muscle
39	chr11:72335400-72341200	Enhancers	Brain Anterior Caudate	brain
40	chr11:72335400-72346600	Enhancers	Brain Angular Gyrus	brain

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