Variant report

Variant	rs12681639
Chromosome Location	chr8:10448142-10448143
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:13)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:13 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr8:10447712..10448262-chr8:10591419..10591945,2	MCF-7	breast:
2	chr8:10447717..10449945-chr8:10695392..10697388,2	MCF-7	breast:
3	chr8:10447388..10448227-chr8:10671479..10672292,5	MCF-7	breast:
4	chr8:10447015..10448532-chr8:10696136..10697603,15	K562	blood:
5	chr8:10447720..10448261-chr8:10675847..10676686,2	K562	blood:
6	chr8:10447282..10448390-chr8:10682147..10683493,10	MCF-7	breast:
7	chr8:10447312..10448291-chr8:10671241..10672318,3	MCF-7	breast:
8	chr8:10447691..10448293-chr8:10586014..10586821,3	MCF-7	breast:
9	chr8:10446054..10448904-chr8:10503289..10505926,2	K562	blood:
10	chr8:10447404..10448576-chr8:10655982..10656998,11	MCF-7	breast:
11	chr8:10447773..10448295-chr8:10656037..10656649,2	MCF-7	breast:
12	chr8:10447726..10448226-chr8:10680360..10680981,2	K562	blood:
13	chr8:10447286..10448405-chr8:10682073..10684028,19	K562	blood:

No data

Variant related genes	Relation type
ENSG00000258724	Chromatin interaction
ENSG00000254093	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs10089537	0.86[CHB][hapmap];0.84[CHD][hapmap]
rs12543042	1.00[ASW][hapmap];0.80[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.96[GIH][hapmap];0.83[JPT][hapmap];1.00[LWK][hapmap];0.84[MEX][hapmap];1.00[MKK][hapmap];0.86[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[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	nsv1030934	chr8:10065169-10561161	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv1022994	chr8:10190618-10660122	Strong transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
3	nsv539466	chr8:10190618-10660122	Enhancers Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
4	nsv1025557	chr8:10216726-10555187	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
5	nsv917085	chr8:10237508-10828204	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
6	nsv610267	chr8:10268736-10526742	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
7	nsv610268	chr8:10331636-10486652	Bivalent Enhancer Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
8	nsv1025251	chr8:10343591-10488557	Flanking Active TSS Bivalent Enhancer Enhancers Weak transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
9	nsv1015932	chr8:10357101-10597856	Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
10	nsv610269	chr8:10416017-10461484	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent/Poised TSS Active TSS	Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
11	nsv610271	chr8:10438796-10459203	Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Genic enhancers Active TSS	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
12	nsv890351	chr8:10439902-10482372	Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats	Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
13	nsv1031279	chr8:10448142-10501380	Enhancers Active TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	Chromatin interactive region miRNA target site	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs12681639	SGCZ	cis	parietal	SCAN
rs12681639	MFHAS1	cis	cerebellum	SCAN
rs12681639	C14orf4	trans	cerebellum	SCAN
rs12681639	C8orf79	cis	cerebellum	SCAN
rs12681639	C8orf79	cis	parietal	SCAN

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:10439000-10453000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr8:10445200-10450400	Weak transcription	Brain Inferior Temporal Lobe	brain
3	chr8:10446800-10448200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr8:10447400-10449200	Enhancers	Lung	lung
5	chr8:10447800-10448200	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
6	chr8:10447800-10448200	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr8:10447800-10448200	Enhancers	Liver	Liver
8	chr8:10447800-10448200	Bivalent Enhancer	Fetal Stomach	stomach
9	chr8:10447800-10448200	Bivalent Enhancer	Stomach Smooth Muscle	stomach
10	chr8:10447800-10448400	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
11	chr8:10447800-10448600	Enhancers	Adipose Nuclei	Adipose
12	chr8:10447800-10449600	Bivalent Enhancer	Fetal Muscle Leg	muscle
13	chr8:10447800-10449600	Enhancers	HUVEC	blood vessel
14	chr8:10447800-10452000	Bivalent Enhancer	Fetal Muscle Trunk	muscle
15	chr8:10448000-10448200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr8:10448000-10448200	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
17	chr8:10448000-10448200	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr8:10448000-10448200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr8:10448000-10448200	Bivalent Enhancer	Brain Germinal Matrix	brain
20	chr8:10448000-10448200	Flanking Active TSS	Hela-S3	cervix
21	chr8:10448000-10448200	Enhancers	NH-A	brain

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