Variant report

Variant	rs12550827
Chromosome Location	chr8:125555087-125555088
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr8:125554491-125558052	K562	blood:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr8:125485971..125490407-chr8:125553790..125556730,4	MCF-7	breast:
2	chr8:125459427..125466261-chr8:125549985..125555147,10	K562	blood:
3	chr8:125550700..125556653-chr8:126010348..126014681,6	K562	blood:
4	chr8:125520394..125523282-chr8:125554552..125556147,2	MCF-7	breast:
5	chr8:125549460..125555106-chr8:125573452..125578755,9	MCF-7	breast:
6	chr4:83293458..83295359-chr8:125553294..125555708,2	MCF-7	breast:
7	chr8:125460680..125466261-chr8:125549985..125555147,10	K562	blood:

No data

Variant related genes	Relation type
NDUFB9	TF binding region
TATDN1	TF binding region
ENSG00000245149	Chromatin interaction
ENSG00000147687	Chromatin interaction
ENSG00000104549	Chromatin interaction
ENSG00000253513	Chromatin interaction
ENSG00000138668	Chromatin interaction
ENSG00000183665	Chromatin interaction
ENSG00000170873	Chromatin interaction
ENSG00000170881	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10956184	1.00[CHB][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10956185	1.00[ASW][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.89[MEX][hapmap];0.89[MKK][hapmap];0.81[TSI][hapmap];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10956189	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12542260	1.00[ASW][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.89[MEX][hapmap];0.89[MKK][hapmap];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12544211	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12544621	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.89[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12545267	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12546906	0.81[AMR][1000 genomes]
rs12548836	1.00[ASW][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.89[MEX][hapmap];0.89[MKK][hapmap];0.81[TSI][hapmap];1.00[YRI][hapmap];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12550707	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28576577	1.00[LWK][hapmap]
rs4512366	1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4551335	0.85[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4602869	0.81[AMR][1000 genomes]
rs5004281	1.00[ASW][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.89[MEX][hapmap];0.89[MKK][hapmap];0.81[TSI][hapmap];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs56942034	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs57941917	0.94[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62527883	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs62527886	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs62527901	0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62527908	0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62527910	0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6987358	0.80[AMR][1000 genomes]
rs7830325	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7845008	1.00[ASW][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.89[MEX][hapmap];0.89[MKK][hapmap];0.81[TSI][hapmap];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[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	nsv531508	chr8:125390194-125587953	Flanking Active TSS Strong transcription Enhancers Weak transcription ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	84 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12550827	ZHX2	cis	cerebellum	SCAN
rs12550827	ZHX2	cis	parietal	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:125552000-125555400	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr8:125552000-125557400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr8:125552200-125555200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr8:125552200-125555200	Weak transcription	Aorta	Aorta
5	chr8:125552200-125565200	Weak transcription	Small Intestine	intestine
6	chr8:125552200-125565800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr8:125552200-125568600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr8:125552400-125555200	Weak transcription	Placenta	Placenta
9	chr8:125552400-125555400	Weak transcription	Colonic Mucosa	Colon
10	chr8:125552600-125555200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr8:125552600-125555400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
12	chr8:125552600-125556400	Weak transcription	Stomach Mucosa	stomach
13	chr8:125553000-125555200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr8:125553000-125555200	Weak transcription	Muscle Satellite Cultured Cells	--
15	chr8:125553000-125555200	Weak transcription	Fetal Kidney	kidney
16	chr8:125553000-125555400	Weak transcription	Brain Substantia Nigra	brain
17	chr8:125553000-125558800	Genic enhancers	Primary T helper cells fromperipheralblood	blood
18	chr8:125553200-125555200	Weak transcription	H1 Cell Line	embryonic stem cell
19	chr8:125553200-125555200	Weak transcription	Brain Cingulate Gyrus	brain
20	chr8:125553200-125555200	Weak transcription	Esophagus	oesophagus
21	chr8:125553200-125555200	Weak transcription	Fetal Brain Male	brain
22	chr8:125553200-125555200	Weak transcription	Pancreas	Pancrea
23	chr8:125553200-125555200	Weak transcription	Rectal Mucosa Donor 29	rectum
24	chr8:125553200-125555200	Weak transcription	Right Ventricle	heart
25	chr8:125553200-125555200	Weak transcription	HUVEC	blood vessel
26	chr8:125553200-125555400	Weak transcription	Pancreatic Islets	Pancreatic Islet
27	chr8:125553200-125555400	Weak transcription	NHEK	skin
28	chr8:125553200-125555600	Genic enhancers	K562	blood
29	chr8:125553200-125555800	Weak transcription	HMEC	breast
30	chr8:125553200-125556400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr8:125553400-125555600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr8:125553400-125556000	Weak transcription	Psoas Muscle	Psoas
33	chr8:125553400-125557200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr8:125553400-125568000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
35	chr8:125553400-125568200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr8:125553400-125575200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
37	chr8:125553400-125575200	Strong transcription	Fetal Muscle Leg	muscle
38	chr8:125553600-125555400	Weak transcription	Duodenum Smooth Muscle	Duodenum
39	chr8:125553600-125556400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr8:125553600-125566400	Strong transcription	A549	lung
41	chr8:125553600-125566800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
42	chr8:125553800-125555400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr8:125553800-125556000	Genic enhancers	Primary T cells fromperipheralblood	blood
44	chr8:125553800-125556000	Strong transcription	Fetal Intestine Small	intestine
45	chr8:125553800-125557800	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr8:125553800-125575400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
47	chr8:125553800-125581200	Strong transcription	Fetal Brain Female	brain
48	chr8:125554000-125556200	Strong transcription	Fetal Stomach	stomach
49	chr8:125554000-125572400	Strong transcription	Thymus	Thymus
50	chr8:125554000-125574000	Strong transcription	Cortex derived primary cultured neurospheres	brain

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