Variant report

Variant	rs10774589
Chromosome Location	chr12:121689798-121689799
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:121676787..121679151-chr12:121688485..121690169,2	MCF-7	breast:
2	chr12:121685040..121687317-chr12:121689126..121690781,3	K562	blood:

Extended variants
information (count: 38 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10774588	0.85[CEU][hapmap]
rs10849856	0.90[JPT][hapmap]
rs10849861	0.91[AMR][1000 genomes]
rs10849862	0.89[AMR][1000 genomes]
rs11065508	0.89[AMR][1000 genomes]
rs1132780	0.95[MEX][hapmap];0.89[AMR][1000 genomes]
rs1169720	0.90[JPT][hapmap]
rs1169727	0.90[JPT][hapmap]
rs1180051	0.81[CHB][hapmap];0.90[JPT][hapmap]
rs12227729	0.83[AMR][1000 genomes]
rs12227751	0.83[AMR][1000 genomes]
rs12304301	0.89[AMR][1000 genomes]
rs1560568	0.91[MEX][hapmap];0.89[AMR][1000 genomes]
rs1629287	0.90[JPT][hapmap]
rs1653622	0.95[JPT][hapmap]
rs2288692	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2393849	0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2393850	0.86[EUR][1000 genomes]
rs25643	0.90[JPT][hapmap]
rs2668250	0.89[AMR][1000 genomes]
rs2686387	0.90[JPT][hapmap]
rs3794202	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3794203	0.87[AMR][1000 genomes]
rs3794204	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3794208	0.95[MEX][hapmap];0.92[AMR][1000 genomes]
rs58232824	0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7298368	1.00[CEU][hapmap];0.90[JPT][hapmap];0.82[MEX][hapmap];0.82[TSI][hapmap];0.86[EUR][1000 genomes]
rs7975295	0.83[CEU][hapmap];0.92[AMR][1000 genomes]
rs7975297	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7975910	0.92[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv521928	chr12:121041728-121761800	Genic enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
2	nsv560454	chr12:121457073-121745742	Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv1054878	chr12:121519880-121761800	Flanking Active TSS Genic enhancers Strong transcription Weak transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
4	nsv455729	chr12:121525591-121761800	Enhancers Strong transcription Genic enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
5	nsv560455	chr12:121525591-121761800	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
6	nsv1050519	chr12:121552964-121756420	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
7	nsv899564	chr12:121641509-121689798	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
8	nsv899565	chr12:121641509-121698785	Weak transcription Genic enhancers Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs10774589	P2RX4	cis	parietal	SCAN
rs10774589	ZCCHC8	cis	parietal	SCAN
rs10774589	C12orf43	cis	parietal	SCAN
rs10774589	P2RX4	cis	cerebellum	SCAN
rs10774589	PSMD9	cis	parietal	SCAN
rs10774589	P2RX7	cis	parietal	SCAN
rs10774589	POP5	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:121653200-121698800	Weak transcription	Fetal Heart	heart
2	chr12:121662800-121690600	Weak transcription	Fetal Brain Male	brain
3	chr12:121670600-121695000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr12:121674600-121692800	Strong transcription	Cortex derived primary cultured neurospheres	brain
5	chr12:121674600-121704200	Strong transcription	Brain Germinal Matrix	brain
6	chr12:121677400-121695600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr12:121677400-121717000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr12:121677400-121717200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr12:121678600-121690400	Weak transcription	Psoas Muscle	Psoas
10	chr12:121679000-121713000	Strong transcription	Fetal Intestine Large	intestine
11	chr12:121679200-121709200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr12:121679200-121714400	Weak transcription	Right Atrium	heart
13	chr12:121679400-121699000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
14	chr12:121679400-121713800	Strong transcription	Primary neutrophils fromperipheralblood	blood
15	chr12:121679600-121690800	Weak transcription	K562	blood
16	chr12:121679600-121708800	Strong transcription	Fetal Muscle Leg	muscle
17	chr12:121679600-121709200	Strong transcription	Stomach Smooth Muscle	stomach
18	chr12:121679600-121713000	Strong transcription	Liver	Liver
19	chr12:121679600-121732600	Strong transcription	Fetal Intestine Small	intestine
20	chr12:121679800-121690400	Strong transcription	Fetal Stomach	stomach
21	chr12:121679800-121694600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr12:121679800-121703200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr12:121679800-121709000	Strong transcription	Fetal Muscle Trunk	muscle
24	chr12:121679800-121713000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
25	chr12:121679800-121713600	Strong transcription	Monocytes-CD14+_RO01746	blood
26	chr12:121680000-121709800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
27	chr12:121680200-121690600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
28	chr12:121680400-121690600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
29	chr12:121680800-121713800	Strong transcription	Primary monocytes fromperipheralblood	blood
30	chr12:121681000-121709000	Strong transcription	Adipose Nuclei	Adipose
31	chr12:121681000-121712600	Strong transcription	Duodenum Mucosa	Duodenum
32	chr12:121681200-121693400	Strong transcription	Primary T cells fromperipheralblood	blood
33	chr12:121681200-121693800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
34	chr12:121681200-121706400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
35	chr12:121681200-121708800	Strong transcription	HUES6 Cell Line	embryonic stem cell
36	chr12:121681200-121708800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr12:121681200-121708800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr12:121681200-121713600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr12:121681200-121717800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr12:121681400-121708800	Strong transcription	Sigmoid Colon	Sigmoid Colon
41	chr12:121681600-121694000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
42	chr12:121681800-121690600	Weak transcription	NH-A	brain
43	chr12:121681800-121690800	Weak transcription	Fetal Kidney	kidney
44	chr12:121682200-121695000	Weak transcription	Pancreatic Islets	Pancreatic Islet
45	chr12:121684400-121691000	Strong transcription	Fetal Thymus	thymus
46	chr12:121684600-121696000	Strong transcription	Duodenum Smooth Muscle	Duodenum
47	chr12:121684800-121693000	Strong transcription	Brain Hippocampus Middle	brain
48	chr12:121684800-121693400	Strong transcription	HUES48 Cell Line	embryonic stem cell
49	chr12:121684800-121693800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
50	chr12:121684800-121693800	Strong transcription	Left Ventricle	heart

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