Variant report

Variant	rs2280870
Chromosome Location	chr8:65499192-65499193
allele	A/C
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	SUZ12	chr8:65497932-65500143	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr8:65498388-65500182	H1-neurons	neurons:	n/a	n/a
3	BACH1	chr8:65498585-65499234	H1-hESC	embryonic stem cell:	n/a	n/a
4	POLR2A	chr8:65498304-65499967	H1-neurons	neurons:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr8:65492030..65493969-chr8:65497416..65499279,2	K562	blood:

Variant related genes	Relation type
ENSG00000254102	TF binding region
ENSG00000180828	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs10441541	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap]
rs11996600	0.86[EUR][1000 genomes]
rs1451868	0.93[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs1597727	0.85[EUR][1000 genomes]
rs4367588	0.91[CHB][hapmap];0.88[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap]
rs4737675	1.00[ASW][hapmap];0.83[MEX][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap]
rs6990308	0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7009638	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap]
rs7016250	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7831363	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv534001	chr8:64992196-65798776	Enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2280870	CHD7	cis	parietal	SCAN
rs2280870	NRN1	trans	lymphoblastoid	seeQTL
rs2280870	CYP7B1	cis	parietal	SCAN

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:65497800-65499600	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
2	chr8:65498000-65499400	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
3	chr8:65498200-65499800	Bivalent/Poised TSS	Brain Cingulate Gyrus	brain
4	chr8:65498200-65499800	Bivalent/Poised TSS	Brain Hippocampus Middle	brain
5	chr8:65498200-65500000	Bivalent Enhancer	Fetal Muscle Trunk	muscle
6	chr8:65498400-65499200	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
7	chr8:65498400-65499200	Bivalent Enhancer	Primary hematopoietic stem cells	blood
8	chr8:65498400-65499200	Flanking Bivalent TSS/Enh	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr8:65498400-65499200	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr8:65498400-65499200	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr8:65498400-65499200	Bivalent/Poised TSS	Brain Inferior Temporal Lobe	brain
12	chr8:65498400-65499200	Bivalent/Poised TSS	Brain Substantia Nigra	brain
13	chr8:65498400-65499200	Bivalent Enhancer	Fetal Heart	heart
14	chr8:65498400-65499200	Bivalent Enhancer	Fetal Muscle Leg	muscle
15	chr8:65498400-65499400	Bivalent Enhancer	Fetal Lung	lung
16	chr8:65498400-65499600	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
17	chr8:65498400-65499600	Flanking Bivalent TSS/Enh	iPS-20b Cell Line	embryonic stem cell
18	chr8:65498400-65500000	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
19	chr8:65498400-65500200	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
20	chr8:65498400-65500200	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
21	chr8:65498600-65499200	Flanking Bivalent TSS/Enh	NHEK	skin
22	chr8:65498600-65500000	Bivalent Enhancer	Liver	Liver
23	chr8:65498600-65500200	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
24	chr8:65498800-65499200	Flanking Bivalent TSS/Enh	Fetal Brain Male	brain
25	chr8:65498800-65499400	Bivalent Enhancer	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr8:65498800-65499400	Flanking Bivalent TSS/Enh	Fetal Brain Female	brain
27	chr8:65498800-65499600	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr8:65498800-65499600	Weak transcription	Pancreas	Pancrea
29	chr8:65498800-65500000	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
30	chr8:65499000-65499200	Flanking Bivalent TSS/Enh	ES-I3 Cell Line	embryonic stem cell
31	chr8:65499000-65499200	Bivalent Enhancer	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
32	chr8:65499000-65499200	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr8:65499000-65499200	Bivalent Enhancer	GM12878-XiMat	blood
34	chr8:65499000-65499400	Flanking Bivalent TSS/Enh	HUES48 Cell Line	embryonic stem cell
35	chr8:65499000-65499400	Bivalent Enhancer	Brain Dorsolateral Prefrontal Cortex	brain
36	chr8:65499000-65499600	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell

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