Variant report

Variant	rs10956189
Chromosome Location	chr8:125567019-125567020
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr8:125560928..125566588-chr8:125566852..125577107,17	MCF-7	breast:
2	chr8:125547667..125554911-chr8:125566055..125572382,17	MCF-7	breast:
3	chr8:125565320..125567312-chr8:125567324..125569326,2	MCF-7	breast:
4	chr8:125566782..125568415-chr8:125579586..125582316,2	K562	blood:
5	chr8:125542543..125545366-chr8:125564681..125567341,2	MCF-7	breast:
6	chr8:125566051..125568002-chr8:125591636..125593613,2	K562	blood:

Variant related genes	Relation type
ENSG00000147687	Chromatin interaction
ENSG00000147684	Chromatin interaction
ENSG00000170873	Chromatin interaction
ENSG00000272486	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10956184	1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];0.83[MEX][hapmap];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10956185	1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.89[MEX][hapmap];0.89[MKK][hapmap];0.80[TSI][hapmap];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12542260	1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.89[MEX][hapmap];0.89[MKK][hapmap];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12544211	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12544621	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.89[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12545267	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12546906	0.80[AMR][1000 genomes]
rs12548836	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.89[MEX][hapmap];0.89[MKK][hapmap];0.80[TSI][hapmap];1.00[YRI][hapmap];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12550707	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12550827	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]
rs28576577	1.00[LWK][hapmap]
rs4512366	1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];0.84[MEX][hapmap];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4551335	0.85[CHB][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4602869	0.80[AMR][1000 genomes]
rs5004281	1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.89[MEX][hapmap];0.89[MKK][hapmap];0.80[TSI][hapmap];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs56942034	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs57941917	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62527883	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs62527886	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs62527901	0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62527908	0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62527910	0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7830325	1.00[CHB][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7845008	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.89[MEX][hapmap];0.89[MKK][hapmap];0.80[TSI][hapmap];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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
2	nsv465801	chr8:125565328-125576681	Transcr. at gene 5' and 3' ZNF genes & repeats Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
3	nsv612145	chr8:125565328-125576681	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
4	nsv525649	chr8:125565328-125600818	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10956189	ZHX2	cis	parietal	SCAN
rs10956189	TRMT12	cis	multi-tissue	Pritchard
rs10956189	ZHX2	cis	cerebellum	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:125552200-125568600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr8:125553400-125568000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr8:125553400-125568200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr8:125553400-125575200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
5	chr8:125553400-125575200	Strong transcription	Fetal Muscle Leg	muscle
6	chr8:125553800-125575400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
7	chr8:125553800-125581200	Strong transcription	Fetal Brain Female	brain
8	chr8:125554000-125572400	Strong transcription	Thymus	Thymus
9	chr8:125554000-125574000	Strong transcription	Cortex derived primary cultured neurospheres	brain
10	chr8:125554200-125568600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr8:125554200-125570000	Strong transcription	Fetal Thymus	thymus
12	chr8:125554200-125576200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr8:125554400-125567400	Strong transcription	Colon Smooth Muscle	Colon
14	chr8:125554400-125568200	Strong transcription	Duodenum Mucosa	Duodenum
15	chr8:125554400-125568400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr8:125554400-125569000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr8:125554400-125574200	Strong transcription	Fetal Muscle Trunk	muscle
18	chr8:125554400-125575400	Strong transcription	Primary B cells from cord blood	blood
19	chr8:125554400-125576200	Strong transcription	Fetal Intestine Large	intestine
20	chr8:125554600-125568000	Strong transcription	Rectal Smooth Muscle	rectum
21	chr8:125554600-125574000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr8:125554600-125575000	Strong transcription	Primary B cells from peripheral blood	blood
23	chr8:125554600-125575800	Strong transcription	Stomach Smooth Muscle	stomach
24	chr8:125554800-125569200	Strong transcription	Rectal Mucosa Donor 31	rectum
25	chr8:125555000-125568200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr8:125555200-125569000	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
27	chr8:125555200-125574000	Strong transcription	Placenta	Placenta
28	chr8:125555200-125575000	Strong transcription	Rectal Mucosa Donor 29	rectum
29	chr8:125555200-125575200	Strong transcription	Brain Cingulate Gyrus	brain
30	chr8:125555400-125568200	Strong transcription	Duodenum Smooth Muscle	Duodenum
31	chr8:125555600-125574200	Strong transcription	Primary T cells from cord blood	blood
32	chr8:125556000-125574200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
33	chr8:125556200-125575000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
34	chr8:125556800-125567200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
35	chr8:125556800-125576800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr8:125557000-125568000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr8:125557000-125568600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr8:125557000-125569200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr8:125557000-125572400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr8:125557600-125567600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
41	chr8:125558000-125567400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr8:125558000-125575600	Weak transcription	Stomach Mucosa	stomach
43	chr8:125558200-125568600	Strong transcription	Sigmoid Colon	Sigmoid Colon
44	chr8:125558200-125573600	Strong transcription	Skeletal Muscle Male	skeletal muscle
45	chr8:125558400-125569200	Strong transcription	Primary monocytes fromperipheralblood	blood
46	chr8:125558800-125573200	Strong transcription	Monocytes-CD14+_RO01746	blood
47	chr8:125559000-125568600	Strong transcription	Brain Angular Gyrus	brain
48	chr8:125559000-125572600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
49	chr8:125559200-125572400	Strong transcription	Lung	lung
50	chr8:125559600-125567400	Strong transcription	Primary T helper memory cells from peripheral blood 2	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links