Variant report

Variant	rs12001425
Chromosome Location	chr9:110094805-110094806
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:110094116..110096830-chr9:110102084..110104724,3	K562	blood:
2	chr9:110094116..110096830-chr9:110102981..110104724,2	K562	blood:
3	chr9:110090174..110092752-chr9:110094331..110096920,2	MCF-7	breast:
4	chr9:110086278..110088143-chr9:110093420..110094981,2	K562	blood:
5	chr9:110081713..110085452-chr9:110093705..110096691,3	MCF-7	breast:

Extended variants
information (count: 27 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10978789	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10978793	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11573631	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11573652	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11573655	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11573700	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12001235	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12004883	1.00[CHB][hapmap]
rs12005299	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12005522	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16912372	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17724694	1.00[EUR][1000 genomes]
rs56091145	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62567660	0.84[EUR][1000 genomes]
rs62567661	0.84[EUR][1000 genomes]
rs62567691	0.84[EUR][1000 genomes]
rs62567693	0.84[EUR][1000 genomes]
rs62567694	0.84[EUR][1000 genomes]
rs62567696	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62567704	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62567738	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62569400	0.84[ASN][1000 genomes]
rs73668766	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs73668780	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7859324	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869351	chr9:109593212-110191170	Active TSS Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	nsv530948	chr9:109760752-110413602	Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:110058600-110098600	Weak transcription	Small Intestine	intestine
2	chr9:110065600-110098600	Strong transcription	Dnd41	blood
3	chr9:110070200-110104400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr9:110070400-110099400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr9:110071400-110103000	Weak transcription	Stomach Mucosa	stomach
6	chr9:110079400-110097400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr9:110079600-110095800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr9:110079600-110098800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr9:110079800-110097600	Strong transcription	HSMM	muscle
10	chr9:110079800-110098000	Strong transcription	HUES6 Cell Line	embryonic stem cell
11	chr9:110080000-110096800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
12	chr9:110080200-110097200	Strong transcription	Primary T helper cells fromperipheralblood	blood
13	chr9:110080600-110097000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
14	chr9:110080600-110097400	Strong transcription	Primary B cells from cord blood	blood
15	chr9:110080600-110097800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr9:110084000-110096600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr9:110084000-110097800	Strong transcription	Hela-S3	cervix
18	chr9:110084800-110098800	Strong transcription	HUES64 Cell Line	embryonic stem cell
19	chr9:110085400-110097800	Strong transcription	Liver	Liver
20	chr9:110086200-110097200	Strong transcription	HepG2	liver
21	chr9:110086200-110097600	Strong transcription	NHLF	lung
22	chr9:110087200-110098600	Strong transcription	Monocytes-CD14+_RO01746	blood
23	chr9:110087400-110095000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr9:110087400-110097200	Strong transcription	Primary monocytes fromperipheralblood	blood
25	chr9:110087600-110103400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
26	chr9:110088200-110096600	Strong transcription	NHDF-Ad	bronchial
27	chr9:110088400-110097200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr9:110088400-110097800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr9:110088400-110097800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr9:110088400-110098800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr9:110088400-110101400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
32	chr9:110088600-110095000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
33	chr9:110088600-110095200	Weak transcription	Brain Cingulate Gyrus	brain
34	chr9:110088600-110097000	Strong transcription	GM12878-XiMat	blood
35	chr9:110088600-110098200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr9:110088600-110098400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr9:110088600-110098600	Weak transcription	Fetal Brain Male	brain
38	chr9:110088600-110101600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr9:110089000-110096800	Strong transcription	Primary T helper cells PMA-I stimulated	--
40	chr9:110089000-110097000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr9:110089600-110097000	Strong transcription	HUES48 Cell Line	embryonic stem cell
42	chr9:110089600-110097800	Strong transcription	Osteobl	bone
43	chr9:110089600-110098000	Strong transcription	K562	blood
44	chr9:110089800-110099400	Strong transcription	Placenta	Placenta
45	chr9:110090000-110097200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
46	chr9:110090200-110096200	Strong transcription	Primary B cells from peripheral blood	blood
47	chr9:110090200-110097000	Strong transcription	Primary hematopoietic stem cells	blood
48	chr9:110090200-110097600	Strong transcription	Primary T cells fromperipheralblood	blood
49	chr9:110090200-110097600	Strong transcription	Fetal Thymus	thymus
50	chr9:110090200-110097800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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