Variant report

Variant	rs12095861
Chromosome Location	chr1:190445614-190445615
allele	A/C/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	POLR2A	chr1:190445592-190445734	MCF10A-Er-Src	breast:	n/a	n/a

Variant related genes	Relation type
BRINP3	TF binding region
ENSG00000237457	TF binding region
ENSG00000241505	TF binding region

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs10920717	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs10920721	1.00[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12068330	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12068796	1.00[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12073477	0.86[AFR][1000 genomes]
rs12076051	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12095425	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs12096714	0.86[AFR][1000 genomes]
rs28712328	0.83[AFR][1000 genomes];1.00[AMR][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	nsv932040	chr1:190005334-190914580	Enhancers Active TSS Bivalent/Poised TSS Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	nsv872758	chr1:190351677-190510003	Bivalent Enhancer Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv872759	chr1:190371671-190446098	Enhancers Bivalent/Poised TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv872760	chr1:190377988-190577336	Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Enhancers Bivalent Enhancer Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv872761	chr1:190389741-190485034	Flanking Bivalent TSS/Enh Active TSS Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv872762	chr1:190389741-190510003	Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Strong transcription Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
7	nsv872763	chr1:190389741-190531642	Active TSS Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
8	nsv872764	chr1:190399946-190531642	Flanking Active TSS Active TSS Weak transcription Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
9	nsv872765	chr1:190418653-190464647	Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
10	nsv466750	chr1:190433413-190496007	Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Flanking Active TSS Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
11	nsv548551	chr1:190433413-190496007	Bivalent Enhancer Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
12	nsv466761	chr1:190433413-190545283	Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Weak transcription Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
13	nsv548552	chr1:190433413-190545283	Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:190440000-190448800	Active TSS	Duodenum Mucosa	Duodenum
2	chr1:190440200-190448800	Active TSS	Fetal Intestine Large	intestine
3	chr1:190440800-190448600	Active TSS	Rectal Mucosa Donor 31	rectum
4	chr1:190440800-190448800	Active TSS	Rectal Mucosa Donor 29	rectum
5	chr1:190441000-190445800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr1:190441200-190448600	Active TSS	Fetal Intestine Small	intestine
7	chr1:190441200-190448600	Active TSS	Right Atrium	heart
8	chr1:190443000-190449600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
9	chr1:190443200-190445800	Active TSS	Fetal Heart	heart
10	chr1:190443400-190445800	Active TSS	Rectal Smooth Muscle	rectum
11	chr1:190443600-190446000	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
12	chr1:190443800-190445800	Flanking Bivalent TSS/Enh	HUVEC	blood vessel
13	chr1:190444800-190447200	Bivalent/Poised TSS	Brain Cingulate Gyrus	brain
14	chr1:190445000-190445800	Bivalent/Poised TSS	Brain Substantia Nigra	brain
15	chr1:190445000-190446600	Bivalent/Poised TSS	Brain Hippocampus Middle	brain
16	chr1:190445000-190447600	Active TSS	Brain Angular Gyrus	brain
17	chr1:190445200-190446000	Active TSS	Cortex derived primary cultured neurospheres	brain
18	chr1:190445200-190446200	Flanking Active TSS	Brain Germinal Matrix	brain
19	chr1:190445200-190447200	Weak transcription	Gastric	stomach
20	chr1:190445200-190449000	Active TSS	Brain Inferior Temporal Lobe	brain
21	chr1:190445400-190445800	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
22	chr1:190445400-190445800	Flanking Active TSS	Fetal Brain Male	brain
23	chr1:190445400-190446200	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
24	chr1:190445400-190446600	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr1:190445400-190446800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr1:190445400-190446800	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
27	chr1:190445400-190446800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr1:190445400-190446800	Weak transcription	Sigmoid Colon	Sigmoid Colon
29	chr1:190445400-190447200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr1:190445400-190447200	Weak transcription	Pancreas	Pancrea
31	chr1:190445400-190447200	Weak transcription	NHLF	lung
32	chr1:190445600-190445800	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
33	chr1:190445600-190445800	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr1:190445600-190445800	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell
35	chr1:190445600-190445800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr1:190445600-190445800	Active TSS	Fetal Stomach	stomach
37	chr1:190445600-190446200	Bivalent/Poised TSS	Brain Anterior Caudate	brain
38	chr1:190445600-190446600	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
39	chr1:190445600-190446600	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
40	chr1:190445600-190446600	Weak transcription	Colonic Mucosa	Colon
41	chr1:190445600-190446800	Active TSS	Fetal Brain Female	brain
42	chr1:190445600-190447000	Weak transcription	Right Ventricle	heart

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