Variant report

Variant	rs60458886
Chromosome Location	chr10:50324370-50324371
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	EP300	chr10:50324270-50324459	GM12878	blood:	n/a	n/a
2	PBX3	chr10:50324282-50324479	GM12878	blood:	n/a	chr10:50324418-50324427
3	MAX	chr10:50324362-50324598	NB4	blood:	n/a	chr10:50324498-50324508
4	BATF	chr10:50324193-50324568	GM12878	blood:	n/a	n/a
5	RCOR1	chr10:50323458-50324528	IMR90	lung:	n/a	n/a
6	CHD2	chr10:50324251-50324451	GM12878	blood:	n/a	n/a
7	RUNX3	chr10:50324178-50324551	GM12878	blood:	n/a	n/a
8	RUNX3	chr10:50324185-50324592	GM12878	blood:	n/a	n/a
9	EP300	chr10:50324211-50324478	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:50322283..50325786-chr10:50341748..50344745,3	K562	blood:

Variant related genes	Relation type
VSTM4	TF binding region
ENSG00000172538	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs56678944	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57192152	0.87[AMR][1000 genomes]
rs58468873	0.87[AMR][1000 genomes]
rs58989233	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59250742	0.87[AMR][1000 genomes]
rs59481238	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59598256	1.00[AMR][1000 genomes]
rs60282422	0.87[AMR][1000 genomes]
rs61403024	0.87[AMR][1000 genomes]
rs7080920	0.87[AMR][1000 genomes]
rs73302775	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73304781	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv831866	chr10:50165180-50335276	Enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	10 gene(s)	inside rSNPs	diseases
2	esv2761593	chr10:50276812-50336129	Weak transcription Genic enhancers Flanking Active TSS Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv895375	chr10:50306386-51028871	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
4	esv1824894	chr10:50309905-50340304	Genic enhancers Flanking Active TSS Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv534410	chr10:50317458-50826916	Weak transcription Bivalent Enhancer Enhancers Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
6	nsv550817	chr10:50319387-50328494	Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
7	esv3497465	chr10:50322646-50324644	Active TSS Enhancers Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
8	esv3497466	chr10:50322646-50324644	Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Weak transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
9	esv1796109	chr10:50323229-50326725	Bivalent/Poised TSS Bivalent Enhancer Active TSS Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
10	esv1802290	chr10:50323229-50326725	Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
11	esv1818143	chr10:50323229-50332930	Bivalent Enhancer Enhancers Active TSS Bivalent/Poised TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:50322200-50324600	Active TSS	Brain Cingulate Gyrus	brain
2	chr10:50322800-50324400	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
3	chr10:50322800-50324600	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
4	chr10:50323800-50326200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr10:50323800-50327800	Weak transcription	NH-A	brain
6	chr10:50324000-50324400	Bivalent Enhancer	Fetal Muscle Leg	muscle
7	chr10:50324000-50324800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr10:50324000-50325000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr10:50324000-50325000	Enhancers	Ovary	ovary
10	chr10:50324000-50325200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr10:50324000-50325200	Weak transcription	Adipose Nuclei	Adipose
12	chr10:50324000-50325400	Enhancers	Liver	Liver
13	chr10:50324000-50325600	Weak transcription	Brain Angular Gyrus	brain
14	chr10:50324000-50325800	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr10:50324000-50327200	Enhancers	Fetal Thymus	thymus
16	chr10:50324000-50328200	Weak transcription	HSMMtube	muscle
17	chr10:50324000-50343600	Weak transcription	Right Atrium	heart
18	chr10:50324200-50324600	Weak transcription	Brain Hippocampus Middle	brain
19	chr10:50324200-50325000	Enhancers	Fetal Muscle Trunk	muscle
20	chr10:50324200-50325400	Weak transcription	Skeletal Muscle Female	skeletal muscle
21	chr10:50324200-50325400	Weak transcription	Stomach Smooth Muscle	stomach
22	chr10:50324200-50325600	Weak transcription	K562	blood
23	chr10:50324200-50326600	Weak transcription	Primary hematopoietic stem cells	blood
24	chr10:50324200-50328400	Weak transcription	Fetal Stomach	stomach

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links