Variant report

Variant	rs7487682
Chromosome Location	chr12:48579665-48579666
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	TAF1	chr12:48578529-48579776	H1-neurons	neurons:	n/a	n/a
2	REST	chr12:48576228-48580563	H1-neurons	neurons:	n/a	chr12:48577348-48577357 chr12:48576911-48576924
3	CTCF	chr12:48579660-48579810	GM12872	blood:	n/a	n/a
4	E2F6	chr12:48578836-48579762	H1-hESC	embryonic stem cell:	n/a	n/a
5	POLR2A	chr12:48576694-48580496	H1-neurons	neurons:	n/a	n/a
6	POLR2A	chr12:48578332-48580491	H1-neurons	neurons:	n/a	n/a
7	CTCF	chr12:48579640-48579790	GM12867	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:48578276..48580987-chr12:48583534..48585807,2	K562	blood:
2	chr12:48576960..48580173-chr12:48592129..48594089,3	MCF-7	breast:
3	chr12:48549998..48552316-chr12:48577251..48580205,2	MCF-7	breast:
4	chr12:48577879..48579746-chr12:48586715..48588244,2	K562	blood:

Variant related genes	Relation type
ASB8	TF binding region
ENSG00000269514	Chromatin interaction
ENSG00000177981	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10875718	0.83[GIH][hapmap]
rs10875719	0.88[GIH][hapmap]
rs10875743	0.81[CEU][hapmap];1.00[CHB][hapmap]
rs10875749	0.88[CEU][hapmap];1.00[CHB][hapmap]
rs10875753	1.00[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.82[TSI][hapmap]
rs1107654	1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.85[MEX][hapmap];0.93[MKK][hapmap];0.83[TSI][hapmap]
rs11168408	0.81[CEU][hapmap];1.00[CHB][hapmap]
rs11168428	0.88[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.82[TSI][hapmap]
rs11168437	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.82[TSI][hapmap]
rs11168441	1.00[CHB][hapmap];1.00[YRI][hapmap]
rs11168460	1.00[CHB][hapmap];0.88[YRI][hapmap]
rs12228750	0.81[CEU][hapmap];1.00[CHB][hapmap]
rs12368659	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap]
rs12816820	0.88[CEU][hapmap];1.00[CHB][hapmap];0.89[YRI][hapmap]
rs1476607	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.82[TSI][hapmap]
rs2051851	0.80[CEU][hapmap]
rs2054905	1.00[CHB][hapmap]
rs2408955	0.82[GIH][hapmap]
rs2450994	1.00[CHD][hapmap];0.88[GIH][hapmap];0.85[MEX][hapmap]
rs2468943	0.81[GIH][hapmap]
rs2634681	1.00[CHD][hapmap];0.88[GIH][hapmap];0.85[MEX][hapmap]
rs2634684	1.00[CHD][hapmap];0.88[GIH][hapmap];0.85[MEX][hapmap]
rs2732448	1.00[CHD][hapmap];0.88[GIH][hapmap];0.85[MEX][hapmap]
rs2732457	1.00[CHD][hapmap];0.88[GIH][hapmap];0.85[MEX][hapmap]
rs2732466	1.00[CHD][hapmap];0.88[GIH][hapmap];0.85[MEX][hapmap]
rs2732480	0.83[GIH][hapmap]
rs2732481	1.00[CHD][hapmap];0.88[GIH][hapmap]
rs2732484	1.00[CHD][hapmap];0.88[GIH][hapmap];0.85[MEX][hapmap]
rs3997	0.81[CEU][hapmap]
rs4760612	1.00[CHB][hapmap];0.88[YRI][hapmap]
rs4760679	0.81[CEU][hapmap];1.00[CHB][hapmap]
rs6580650	0.88[ASW][hapmap];0.81[CEU][hapmap];0.90[GIH][hapmap]
rs7139330	1.00[CHB][hapmap]
rs7297824	1.00[CHB][hapmap]
rs7301003	0.88[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.82[TSI][hapmap]
rs7307566	1.00[CHB][hapmap];0.88[YRI][hapmap]
rs7315820	1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.85[MEX][hapmap];0.89[MKK][hapmap];0.87[TSI][hapmap]
rs7486941	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs7975632	0.81[CEU][hapmap];1.00[CHB][hapmap];0.90[GIH][hapmap]
rs8716	0.88[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.82[TSI][hapmap];0.88[YRI][hapmap]
rs923397	1.00[CHD][hapmap];0.88[GIH][hapmap];0.85[MEX][hapmap]
rs973398	0.81[CEU][hapmap];1.00[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758307	chr12:48429702-48825499	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
2	esv2759898	chr12:48429702-48825499	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
3	nsv8971	chr12:48536526-48758501	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers 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 target site	39 gene(s)	inside rSNPs	diseases
4	esv34439	chr12:48541757-48779562	Bivalent/Poised TSS Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
5	esv2757502	chr12:48547128-48779562	Genic enhancers Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
6	esv33956	chr12:48565643-48645561	Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Enhancers ZNF genes & repeats Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs7487682	ZNF641	cis	cerebellum	SCAN
rs7487682	H1FNT	cis	Muscle Skeletal	GTEx
rs7487682	TMEM131	trans	parietal	SCAN
rs7487682	DDX23	cis	parietal	SCAN
rs7487682	ADAMTS20	cis	cerebellum	SCAN

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:48576600-48580400	Active TSS	Brain Inferior Temporal Lobe	brain
2	chr12:48576800-48580000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
3	chr12:48578000-48580000	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
4	chr12:48578000-48580400	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr12:48578200-48580400	Enhancers	Esophagus	oesophagus
6	chr12:48578400-48580000	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr12:48578400-48580400	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr12:48578600-48579800	Active TSS	Fetal Brain Male	brain
9	chr12:48578600-48580000	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr12:48578600-48580200	Active TSS	Brain Angular Gyrus	brain
11	chr12:48578600-48580400	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr12:48578800-48579800	Enhancers	Breast Myoepithelial Primary Cells	Breast
13	chr12:48578800-48579800	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr12:48578800-48580000	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
15	chr12:48578800-48580000	Bivalent Enhancer	Fetal Muscle Leg	muscle
16	chr12:48578800-48580000	Bivalent Enhancer	NHEK	skin
17	chr12:48579000-48579800	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
18	chr12:48579000-48579800	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
19	chr12:48579000-48580000	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
20	chr12:48579000-48580400	Bivalent Enhancer	GM12878-XiMat	blood
21	chr12:48579200-48579800	Flanking Active TSS	Brain Anterior Caudate	brain
22	chr12:48579200-48580000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr12:48579200-48580000	Bivalent Enhancer	H9 Cell Line	embryonic stem cell
24	chr12:48579200-48580000	Bivalent Enhancer	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr12:48579200-48580400	Active TSS	Brain Cingulate Gyrus	brain
26	chr12:48579400-48579800	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
27	chr12:48579400-48579800	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr12:48579400-48580000	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell
29	chr12:48579400-48580200	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
30	chr12:48579400-48580400	Bivalent Enhancer	HSMM	muscle
31	chr12:48579600-48579800	Flanking Bivalent TSS/Enh	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr12:48579600-48579800	Bivalent/Poised TSS	Brain Germinal Matrix	brain
33	chr12:48579600-48579800	Bivalent Enhancer	Duodenum Mucosa	Duodenum
34	chr12:48579600-48580000	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr12:48579600-48580200	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
36	chr12:48579600-48580200	Bivalent Enhancer	Hela-S3	cervix
37	chr12:48579600-48580400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
38	chr12:48579600-48580400	Flanking Active TSS	Fetal Brain Female	brain

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